From d53c70c1f2eb71077086ca7ad13eb59158d1351b Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Fri, 19 Oct 2012 14:39:37 -0500 Subject: Reindented genSelectDatasetJS as gen_select_dataset --- wqflask/maintenance/gen_select_dataset.py | 640 ++++++++++++++++++++++++++++++ 1 file changed, 640 insertions(+) create mode 100644 wqflask/maintenance/gen_select_dataset.py (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py new file mode 100644 index 00000000..7d2605c1 --- /dev/null +++ b/wqflask/maintenance/gen_select_dataset.py @@ -0,0 +1,640 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) +# +# Created by GeneNetwork Core Team 2010/08/10 +# +# Last updated by NL 2011/01/27 + +# created by Ning Liu 07/01/2010 +# This script is to generate selectDatasetMenu.js file for cascade menu in the main search page http://www.genenetwork.org/. +# This script will be run automatically every one hour or manually when database has been changed . + +from __future__ import print_function, division + +import sys, os + +current_file_name = __file__ +pathname = os.path.dirname( current_file_name ) +abs_path = os.path.abspath(pathname) +sys.path.insert(0, abs_path + '/..') + +import MySQLdb +import os +import string +import time +import datetime + +from base import template +from base import webqtlConfig + +################################################################################# +# input: searchArray, targetValue +# function: retrieve index info of target value in designated array (searchArray) +# output: return index info +################################################################################## +def getIndex(searchArray=None, targetValue=None): + for index in range(len(searchArray)): + if searchArray[index][0]==targetValue: + return index + +# build MySql database connection +con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) +cursor = con.cursor() + +# create js_select.js file +fileHandler = open(webqtlConfig.HTMLPATH + 'javascript/selectDatasetMenu.js', 'w') + +# define SpeciesString, GroupString, TypeString, DatabasingString, LinkageString for output +# outputSpeciesStr is for building Species Array(sArr) in js file; outputGroupStr is for Group Array(gArr) +# outputTypeStr is for Type Array(tArr); outputDatabaseStr is for Database Array(dArr) +# outputLinkStr is for Linkage Array(lArr) +outputTimeStr ="/* Generated Date : %s , Time : %s */ \n" % (datetime.date.today(),time.strftime("%H:%M ", time.localtime())) +outputTimeStr ="" +outputSpeciesStr ='var sArr = [\n{txt:\'\',val:\'\'},\n' +outputGroupStr ='var gArr = [\n{txt:\'\',val:\'\'},\n' +outputTypeStr ='var tArr = [\n{txt:\'\',val:\'\'},\n' +outputDatabaseStr ='var dArr = [\n{txt:\'\',val:\'\'},\n' +outputLinkStr ='var lArr = [\n null,\n' + +# built speices array in js file for select menu in the main search page http://www.genenetwork.org/ +cursor.execute("select Name, MenuName from Species order by OrderId") +speciesResult = cursor.fetchall() +speciesTotalResult = list(speciesResult) +speciesResultsTotalNum = cursor.rowcount +if speciesResultsTotalNum >0: + for speciesItem in speciesResult: + speciesVal = speciesItem[0] + speciesTxt = speciesItem[1] + outputSpeciesStr += '{txt:\'%s\',val:\'%s\'},\n'%(speciesTxt,speciesVal) +# 'All Species' option for 'Species' select menu +outputSpeciesStr +='{txt:\'All Species\',val:\'All Species\'}];\n\n' +#speciesTotalResult is a list which inclues all species' options +speciesTotalResult.append(('All Species','All Species')) + +# built group array in js file for select menu in the main search page http://www.genenetwork.org/ +cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name") +groupResults = cursor.fetchall() +groupTotalResults = list(groupResults) +groupResultsTotalNum = cursor.rowcount +if groupResultsTotalNum > 0: + for groupItem in groupResults: + groupVal = groupItem[0] + groupTxt = groupItem[1] + outputGroupStr += '{txt:\'%s\',val:\'%s\'},\n'%(groupTxt,groupVal) +# add 'All Groups' option for 'Group' select menu +outputGroupStr +='{txt:\'All Groups\',val:\'all groups\'}];\n\n' +# groupTotalResults is a list which inclues all groups' options +groupTotalResults.append(('all groups','All Groups')) + +# built type array in js file for select menu in the main search page http://www.genenetwork.org/ +cross = groupVal +cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (webqtlConfig.PUBLICTHRESH)) +typeResults = cursor.fetchall() +typeTotalResults = list(typeResults) +typeResultsTotalNum = cursor.rowcount +if typeResultsTotalNum > 0: + for typeItem in typeResults: + typeVal = typeItem[0] + typeTxt = typeItem[1] + outputTypeStr += '{txt:\'%s\',val:\'%s\'},\n'%(typeTxt,typeVal) +# add 'Phenotypes' and 'Genotypes' options for 'Type' select menu +outputTypeStr +='{txt:\'Phenotypes\',val:\'Phenotypes\'},\n' +outputTypeStr +='{txt:\'Genotypes\',val:\'Genotypes\'}];\n\n' +# typeTotalResults is a list which inclues all types' options +typeTotalResults.append(('Phenotypes','Phenotypes')) +typeTotalResults.append(('Genotypes','Genotypes')) + +# built dataset array in js file for select menu in the main search page http://www.genenetwork.org/ +tissue = typeVal +cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (webqtlConfig.PUBLICTHRESH)) +datasetResults = cursor.fetchall() +datasetTotalResults = list(datasetResults) +datasetResultsTotalNum = cursor.rowcount +if datasetResultsTotalNum > 0: + for datasetItem in datasetResults: + datasetVal = datasetItem[0] + datasetTxt = datasetItem[1] + outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal) + +# This part is to built linkage array in js file, the linkage is among Species, Group, Type and Database. +# The format of linkage array is [speciesIndex, groupIndex, typeIndex, databaseIndex] +if speciesResultsTotalNum >0: + for speciesItem in speciesResult: + speciesVal = speciesItem[0] + sIndex = getIndex(searchArray=speciesTotalResult,targetValue=speciesVal)+1 + + # retrieve group info based on specie + cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and Species.Name='%s' and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name" % speciesVal) + groupResults = cursor.fetchall() + groupResultsNum = cursor.rowcount + + if groupResultsNum > 0: + for groupItem in groupResults: + groupVal = groupItem[0] + gIndex = getIndex(searchArray=groupTotalResults, targetValue=groupVal)+1 + + cross = groupVal + # if group also exists in PublishFreeze table, then needs to add related Published Phenotypes in Database Array(dArr) and Linkage Array(lArr) + # 'MDP' case is related to 'Mouse Phenome Database' + cursor.execute("select PublishFreeze.Id from PublishFreeze, InbredSet where PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross) + if (cursor.fetchall()): + typeVal = "Phenotypes" + if cross=='MDP': + datasetTxt = "Mouse Phenome Database" + else: + datasetTxt = "%s Published Phenotypes" % cross + datasetVal = "%sPublish" % cross + outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'% (datasetTxt,datasetVal) + datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt)) + + tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1 + dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 + outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) + + # if group also exists in GenoFreeze table, then needs to add related Genotypes in database Array(dArr) + cursor.execute("select GenoFreeze.Id from GenoFreeze, InbredSet where GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross) + if (cursor.fetchall()): + typeVal = "Genotypes" + datasetTxt = "%s Genotypes" % cross + datasetVal = "%sGeno" % cross + outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal) + typeTotalResults.append(('Genotypes','Genotypes')) + datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt)) + + tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1 + dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 + outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) + + # retrieve type(tissue) info based on group + # if cross is equal to 'BXD', then need to seach for 'BXD' and 'BXD300' InbredSet + if cross == "BXD": + cross2 = "BXD', 'BXD300" + else: + cross2 = cross + cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (cross2, webqtlConfig.PUBLICTHRESH)) + typeResults = cursor.fetchall() + typeResultsNum = cursor.rowcount + + if typeResultsNum > 0: + for typeItem in typeResults: + typeVal = typeItem[0] + tIndex = getIndex(searchArray=typeTotalResults, targetValue=typeVal)+1 + # retrieve database(dataset) info based on group(InbredSet) and type(Tissue) + tissue = typeVal + cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and Tissue.name = '%s' and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (cross2, tissue, webqtlConfig.PUBLICTHRESH)) + datasetResults = cursor.fetchall() + datasetResultsNum = cursor.rowcount + + if datasetResultsNum > 0: + for datasetItem in datasetResults: + datasetVal = datasetItem[0] + dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 + outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) + +# add 'All Phenotypes' option for 'Database' select menu +# for 'All Species'option in 'Species' select menu, 'Database' select menu will show 'All Phenotypes' option +outputDatabaseStr += '{txt:\'%s\',val:\'%s\'}];\n\n'%('All Phenotypes','_allPublish') +datasetTotalResults.append(('_allPublish','All Phenotypes')) + +sIndex = getIndex(searchArray=speciesTotalResult,targetValue='All Species')+1 +gIndex = getIndex(searchArray=groupTotalResults, targetValue='all groups')+1 +tIndex = getIndex(searchArray=typeTotalResults,targetValue='Phenotypes')+1 +dIndex = getIndex(searchArray=datasetTotalResults, targetValue='_allPublish')+1 +outputLinkStr +='[%d,%d,%d,%d]];\n\n'%(sIndex,gIndex,tIndex,dIndex) + +# Combine sArr, gArr, tArr, dArr and lArr output string together +outputStr = outputTimeStr+outputSpeciesStr+outputGroupStr+outputTypeStr+outputDatabaseStr+outputLinkStr +outputStr +=''' + +/* +* function: based on different browser use, will have different initial actions; +* Once the index.html page is loaded, this function will be called +*/ +function initialDatasetSelection() +{ + defaultSpecies =getDefaultValue('species'); + defaultSet =getDefaultValue('cross'); + defaultType =getDefaultValue('tissue'); + defaultDB =getDefaultValue('database'); + + if (navigator.userAgent.indexOf('MSIE')>=0) + { + sOptions = fillOptionsForIE(null,defaultSpecies); + var menu0 =""; + document.getElementById('menu0').innerHTML = menu0; + + gOptions = fillOptionsForIE('species',defaultSet); + var menu1 =""; + document.getElementById('menu1').innerHTML =menu1; + + tOptions = fillOptionsForIE('cross',defaultType); + var menu2 =""; + document.getElementById('menu2').innerHTML =menu2; + + dOptions = fillOptionsForIE('tissue',defaultDB); + var menu3 =""; + document.getElementById('menu3').innerHTML =menu3; + + }else{ + fillOptions(null); + } + searchtip(); +} + +/* +* input: selectObjId (designated select menu, such as species, cross, etc... ) +* defaultValue (default Value of species, cross,tissue or database) +* function: special for IE browser,setting options value for select menu dynamically based on linkage array(lArr), +* output: options string +*/ +function fillOptionsForIE(selectObjId,defaultValue) +{ + var options=''; + if(selectObjId==null) + { + var len = sArr.length; + for (var i=1; i < len; i++) { + // setting Species' option + if( sArr[i].val==defaultValue){ + options =options+""; + }else{ + options =options+""; + } + } + }else if(selectObjId=='species') + { + var speciesObj = document.getElementById('species'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get group(cross) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1])) + { + arr[idx++]=lArr[i][1]; + } + } + idx=0; + len = arr.length; + removeOptions("cross"); + for (var i=0; i < len; i++) { + // setting Group's option + if( gArr[arr[i]].val==defaultValue){ + options =options+""; + }else{ + options =options+""; + } + + } + }else if(selectObjId=='cross') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get type(tissue) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2])) + { + arr[idx++]=lArr[i][2]; + } + } + idx=0; + len = arr.length; + removeOptions("tissue"); + for (var i=0; i < len; i++) { + // setting Type's option + if( tArr[arr[i]].val==defaultValue){ + options =options+""; + }else{ + options =options+""; + } + } + + }else if(selectObjId=='tissue') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var typeObj = document.getElementById('tissue'); + + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get dataset(database) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3])) + { + arr[idx++]=lArr[i][3]; + } + } + idx=0; + len = arr.length; + removeOptions("database"); + for (var i=0; i < len; i++) { + // setting Database's option + if( dArr[arr[i]].val==defaultValue){ + options =options+""; + }else{ + options =options+""; + } + } + } + return options; +} +/* +* input: selectObjId (designated select menu, such as species, cross, etc... ) +* function: setting options value for select menu dynamically based on linkage array(lArr) +* output: null +*/ +function fillOptions(selectObjId) +{ + if(selectObjId==null) + { + + var speciesObj = document.getElementById('species'); + var len = sArr.length; + for (var i=1; i < len; i++) { + // setting Species' option + speciesObj.options[i-1] = new Option(sArr[i].txt, sArr[i].val); + } + updateChocie('species'); + + }else if(selectObjId=='species') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get group(cross) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1])) + { + arr[idx++]=lArr[i][1]; + } + } + idx=0; + len = arr.length; + removeOptions("cross"); + for (var i=0; i < len; i++) { + // setting Group's option + groupObj.options[idx++] = new Option(gArr[arr[i]].txt, gArr[arr[i]].val); + } + updateChocie('cross'); + + }else if(selectObjId=='cross') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var typeObj = document.getElementById('tissue'); + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get type(tissue) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2])) + { + arr[idx++]=lArr[i][2]; + } + } + idx=0; + len = arr.length; + removeOptions("tissue"); + for (var i=0; i < len; i++) { + // setting Type's option + typeObj.options[idx++] = new Option(tArr[arr[i]].txt, tArr[arr[i]].val); + } + updateChocie('tissue'); + + }else if(selectObjId=='tissue') + { + var speciesObj = document.getElementById('species'); + var groupObj = document.getElementById('cross'); + var typeObj = document.getElementById('tissue'); + var databaseObj = document.getElementById('database'); + + var len = lArr.length; + var arr = []; + var idx = 0; + for (var i=1; i < len; i++) { + //get dataset(database) info from lArr + if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3])) + { + arr[idx++]=lArr[i][3]; + } + } + idx=0; + len = arr.length; + removeOptions("database"); + for (var i=0; i < len; i++) { + // setting Database's option + databaseObj.options[idx++] = new Option(dArr[arr[i]].txt, dArr[arr[i]].val); + } + updateChocie('database'); + } +} + +/* +* input: arr (targeted array); obj (targeted value) +* function: check whether targeted array contains targeted value or not +* output: return true, if array contains targeted value, otherwise return false +*/ +function Contains(arr,obj) { + var i = arr.length; + while (i--) { + if (arr[i] == obj) { + return true; + } + } + return false; +} + +/* +* input: selectObj (designated select menu, such as species, cross, etc... ) +* function: clear designated select menu's option +* output: null +*/ +function removeOptions(selectObj) { + if (typeof selectObj != 'object'){ + selectObj = document.getElementById(selectObj); + } + var len = selectObj.options.length; + for (var i=0; i < len; i++) { + // clear current selection + selectObj.options[0] = null; + } +} + +/* +* input: selectObjId (designated select menu, such as species, cross, etc... ) +* Value: target value +* function: retrieve Index info of target value in designated array +* output: index info +*/ +function getIndexByValue(selectObjId,val) +{ + if(selectObjId=='species') + { + for(var i=1;i=0){ + //setting option's selected status + Obj.options[idx].selected=true; + //update the following select menu + fillOptions(objId); + }else{ + Obj.options[0].selected=true; + fillOptions(objId); + } +} + +// setting option's selected status based on default setting or cookie setting for Species, Group, Type and Database select menu in the main search page http://www.genenetwork.org/ +function updateChocie(selectObjId){ + + if (selectObjId =='species') + { + defaultSpecies= getDefaultValue('species'); + //setting option's selected status + setChoice('species',defaultSpecies); + }else if (selectObjId =='cross') + { + defaultSet= getDefaultValue('cross'); + //setting option's selected status + setChoice('cross',defaultSet); + }else if (selectObjId =='tissue') + { + defaultType= getDefaultValue('tissue'); + //setting option's selected status + setChoice('tissue',defaultType); + }else if (selectObjId =='database') + { + defaultDB= getDefaultValue('database'); + //setting option's selected status + setChoice('database',defaultDB); + } +} + +//get default value;if cookie exists, then use cookie value, otherwise use default value +function getDefaultValue(selectObjId){ + //define default value + var defaultSpecies = 'mouse' + var defaultSet = 'BXD' + var defaultType = 'Hippocampus' + var defaultDB = 'HC_M2_0606_P' + + if (selectObjId =='species') + { + //if cookie exists, then use cookie value, otherwise use default value + var cookieSpecies = getCookie('defaultSpecies'); + if(cookieSpecies) + { + defaultSpecies= cookieSpecies; + } + return defaultSpecies; + }else if (selectObjId =='cross'){ + var cookieSet = getCookie('defaultSet'); + if(cookieSet){ + defaultSet= cookieSet; + } + return defaultSet; + }else if (selectObjId =='tissue'){ + var cookieType = getCookie('defaultType'); + if(cookieType){ + defaultType= cookieType; + } + return defaultType; + }else if (selectObjId =='database') + { + var cookieDB = getCookie('defaultDB'); + if(cookieDB){ + defaultDB= cookieDB; + } + return defaultDB; + } + +} + +//setting default value into cookies for the dropdown menus: Species,Group, Type, and Database +function setDefault(thisform){ + + setCookie('cookieTest', 'cookieTest', 1); + var cookieTest = getCookie('cookieTest'); + delCookie('cookieTest'); + if (cookieTest){ + var defaultSpecies = thisform.species.value; + setCookie('defaultSpecies', defaultSpecies, 10); + var defaultSet = thisform.cross.value; + setCookie('defaultSet', defaultSet, 10); + var defaultType = thisform.tissue.value; + setCookie('defaultType', defaultType, 10); + var defaultDB = thisform.database.value; + setCookie('defaultDB', defaultDB, 10); + updateChocie('species'); + updateChocie('cross'); + updateChocie('tissue'); + updateChocie('database'); + alert("The current settings are now your default"); + } + else{ + alert("You need to enable Cookies in your browser."); + } +} + +''' +# write all strings' info into selectDatasetMenu.js file +fileHandler.write(outputStr) +fileHandler.close() -- cgit v1.2.3 From bbc5e266213e44af5713f7c9a4bbfd7f1035ad1d Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Fri, 19 Oct 2012 18:26:18 -0500 Subject: Finished gen_select_dataset.py which generates the json file that defines the data structure used for the index page select dropdowns --- misc/notes.txt | 7 +- wqflask/maintenance/gen_select_dataset.py | 724 +-- .../new/javascript/dataset_menu_structure.json | 6792 ++++++++++++++++++++ 3 files changed, 6917 insertions(+), 606 deletions(-) create mode 100644 wqflask/wqflask/static/new/javascript/dataset_menu_structure.json (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/misc/notes.txt b/misc/notes.txt index fab9fac6..c12cd2bb 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -17,11 +17,13 @@ python runserver.py =========================================== -Start screen session +Start screen session: byobu -RD (to start) control-a then :multiuser on control-a then :acladd sam +control-a c to create channel + type: screen -list for sessions screen -r zas1024/25679.byobu @@ -31,6 +33,9 @@ screen -r zas1024/ =========================================== +Start up log: +Go to /tmp and tail -f flask_gn_log + Coffeescript Stuff: coffee -c (filename) diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 7d2605c1..33813051 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -19,622 +19,136 @@ # # # This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 -# -# Last updated by NL 2011/01/27 -# created by Ning Liu 07/01/2010 -# This script is to generate selectDatasetMenu.js file for cascade menu in the main search page http://www.genenetwork.org/. -# This script will be run automatically every one hour or manually when database has been changed . +# This script is to generate the data for the main menus on the home page +# It needs to be run manually when database has been changed . from __future__ import print_function, division -import sys, os +import sys -current_file_name = __file__ -pathname = os.path.dirname( current_file_name ) -abs_path = os.path.abspath(pathname) -sys.path.insert(0, abs_path + '/..') +sys.path.insert(0, "..") import MySQLdb -import os -import string -import time -import datetime - -from base import template -from base import webqtlConfig - -################################################################################# -# input: searchArray, targetValue -# function: retrieve index info of target value in designated array (searchArray) -# output: return index info -################################################################################## -def getIndex(searchArray=None, targetValue=None): - for index in range(len(searchArray)): - if searchArray[index][0]==targetValue: - return index - -# build MySql database connection -con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD) -cursor = con.cursor() -# create js_select.js file -fileHandler = open(webqtlConfig.HTMLPATH + 'javascript/selectDatasetMenu.js', 'w') +import simplejson as json -# define SpeciesString, GroupString, TypeString, DatabasingString, LinkageString for output -# outputSpeciesStr is for building Species Array(sArr) in js file; outputGroupStr is for Group Array(gArr) -# outputTypeStr is for Type Array(tArr); outputDatabaseStr is for Database Array(dArr) -# outputLinkStr is for Linkage Array(lArr) -outputTimeStr ="/* Generated Date : %s , Time : %s */ \n" % (datetime.date.today(),time.strftime("%H:%M ", time.localtime())) -outputTimeStr ="" -outputSpeciesStr ='var sArr = [\n{txt:\'\',val:\'\'},\n' -outputGroupStr ='var gArr = [\n{txt:\'\',val:\'\'},\n' -outputTypeStr ='var tArr = [\n{txt:\'\',val:\'\'},\n' -outputDatabaseStr ='var dArr = [\n{txt:\'\',val:\'\'},\n' -outputLinkStr ='var lArr = [\n null,\n' +from pprint import pformat as pf -# built speices array in js file for select menu in the main search page http://www.genenetwork.org/ -cursor.execute("select Name, MenuName from Species order by OrderId") -speciesResult = cursor.fetchall() -speciesTotalResult = list(speciesResult) -speciesResultsTotalNum = cursor.rowcount -if speciesResultsTotalNum >0: - for speciesItem in speciesResult: - speciesVal = speciesItem[0] - speciesTxt = speciesItem[1] - outputSpeciesStr += '{txt:\'%s\',val:\'%s\'},\n'%(speciesTxt,speciesVal) -# 'All Species' option for 'Species' select menu -outputSpeciesStr +='{txt:\'All Species\',val:\'All Species\'}];\n\n' -#speciesTotalResult is a list which inclues all species' options -speciesTotalResult.append(('All Species','All Species')) - -# built group array in js file for select menu in the main search page http://www.genenetwork.org/ -cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name") -groupResults = cursor.fetchall() -groupTotalResults = list(groupResults) -groupResultsTotalNum = cursor.rowcount -if groupResultsTotalNum > 0: - for groupItem in groupResults: - groupVal = groupItem[0] - groupTxt = groupItem[1] - outputGroupStr += '{txt:\'%s\',val:\'%s\'},\n'%(groupTxt,groupVal) -# add 'All Groups' option for 'Group' select menu -outputGroupStr +='{txt:\'All Groups\',val:\'all groups\'}];\n\n' -# groupTotalResults is a list which inclues all groups' options -groupTotalResults.append(('all groups','All Groups')) - -# built type array in js file for select menu in the main search page http://www.genenetwork.org/ -cross = groupVal -cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (webqtlConfig.PUBLICTHRESH)) -typeResults = cursor.fetchall() -typeTotalResults = list(typeResults) -typeResultsTotalNum = cursor.rowcount -if typeResultsTotalNum > 0: - for typeItem in typeResults: - typeVal = typeItem[0] - typeTxt = typeItem[1] - outputTypeStr += '{txt:\'%s\',val:\'%s\'},\n'%(typeTxt,typeVal) -# add 'Phenotypes' and 'Genotypes' options for 'Type' select menu -outputTypeStr +='{txt:\'Phenotypes\',val:\'Phenotypes\'},\n' -outputTypeStr +='{txt:\'Genotypes\',val:\'Genotypes\'}];\n\n' -# typeTotalResults is a list which inclues all types' options -typeTotalResults.append(('Phenotypes','Phenotypes')) -typeTotalResults.append(('Genotypes','Genotypes')) - -# built dataset array in js file for select menu in the main search page http://www.genenetwork.org/ -tissue = typeVal -cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (webqtlConfig.PUBLICTHRESH)) -datasetResults = cursor.fetchall() -datasetTotalResults = list(datasetResults) -datasetResultsTotalNum = cursor.rowcount -if datasetResultsTotalNum > 0: - for datasetItem in datasetResults: - datasetVal = datasetItem[0] - datasetTxt = datasetItem[1] - outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal) - -# This part is to built linkage array in js file, the linkage is among Species, Group, Type and Database. -# The format of linkage array is [speciesIndex, groupIndex, typeIndex, databaseIndex] -if speciesResultsTotalNum >0: - for speciesItem in speciesResult: - speciesVal = speciesItem[0] - sIndex = getIndex(searchArray=speciesTotalResult,targetValue=speciesVal)+1 - - # retrieve group info based on specie - cursor.execute("select distinct InbredSet.Name, InbredSet.FullName from InbredSet, Species, ProbeFreeze, GenoFreeze, PublishFreeze where InbredSet.SpeciesId= Species.Id and Species.Name='%s' and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id or GenoFreeze.InbredSetId = InbredSet.Id or ProbeFreeze.InbredSetId = InbredSet.Id) order by InbredSet.Name" % speciesVal) - groupResults = cursor.fetchall() - groupResultsNum = cursor.rowcount +from base import webqtlConfig - if groupResultsNum > 0: - for groupItem in groupResults: - groupVal = groupItem[0] - gIndex = getIndex(searchArray=groupTotalResults, targetValue=groupVal)+1 - cross = groupVal - # if group also exists in PublishFreeze table, then needs to add related Published Phenotypes in Database Array(dArr) and Linkage Array(lArr) - # 'MDP' case is related to 'Mouse Phenome Database' - cursor.execute("select PublishFreeze.Id from PublishFreeze, InbredSet where PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross) - if (cursor.fetchall()): - typeVal = "Phenotypes" - if cross=='MDP': - datasetTxt = "Mouse Phenome Database" +# build MySql database connection +Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, + user=webqtlConfig.DB_USER, + passwd=webqtlConfig.DB_PASSWD) +Cursor = Con.cursor() + + +def get_species(): + """Build species list""" + Cursor.execute("select Name, MenuName from Species order by OrderId") + species = list(Cursor.fetchall()) + return species + + +def get_groups(species): + """Build groups list""" + groups = {} + for species_name, _species_full_name in species: + Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet, + Species, + ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s + and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and + (PublishFreeze.InbredSetId = InbredSet.Id + or GenoFreeze.InbredSetId = InbredSet.Id + or ProbeFreeze.InbredSetId = InbredSet.Id) + group by InbredSet.Name + order by InbredSet.Name""", (species_name)) + groups[species_name] = list(Cursor.fetchall()) + return groups + + +def get_types(groups): + """Build types list""" + types = {} + for species, group_dict in groups.iteritems(): + types[species] = {} + for group_name, _group_full_name in group_dict: + # make group an alias to shorten the code + group = types[species][group_name] = [("Phenotypes", "Phenotypes"), + ("Genotypes", "Genotypes")] + Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from + ProbeFreeze, + ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and + ProbeFreeze.InbredSetId = InbredSet.Id and + InbredSet.Name = %s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.public > %s + order by Tissue.Name""", (group_name, webqtlConfig.PUBLICTHRESH)) + group += Cursor.fetchall() + return types + + +def get_datasets(types): + """Build datasets list""" + datasets = {} + for species, group_dict in types.iteritems(): + datasets[species] = {} + for group, type_list in group_dict.iteritems(): + datasets[species][group] = {} + for type_name, type_full_name in type_list: + dataset_text = dataset_value = None + if type_name == "Phenotypes": + dataset_value = "%sPublish" % group + if group == 'MDP': + dataset_text = "Mouse Phenome Database" else: - datasetTxt = "%s Published Phenotypes" % cross - datasetVal = "%sPublish" % cross - outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'% (datasetTxt,datasetVal) - datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt)) - - tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1 - dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 - outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) - - # if group also exists in GenoFreeze table, then needs to add related Genotypes in database Array(dArr) - cursor.execute("select GenoFreeze.Id from GenoFreeze, InbredSet where GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s'" % cross) - if (cursor.fetchall()): - typeVal = "Genotypes" - datasetTxt = "%s Genotypes" % cross - datasetVal = "%sGeno" % cross - outputDatabaseStr += '{txt:\'%s\',val:\'%s\'},\n'%(datasetTxt,datasetVal) - typeTotalResults.append(('Genotypes','Genotypes')) - datasetTotalResults.append(('%s'% datasetVal,'%s' % datasetTxt)) - - tIndex = getIndex(searchArray=typeTotalResults,targetValue=typeVal)+1 - dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 - outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) - - # retrieve type(tissue) info based on group - # if cross is equal to 'BXD', then need to seach for 'BXD' and 'BXD300' InbredSet - if cross == "BXD": - cross2 = "BXD', 'BXD300" + dataset_text = "%s Published Phenotypes" % group + + elif type_name == "Genotypes": + dataset_value = "%sGeno" % group + dataset_text = "%s Genotypes" % group + + if dataset_value: + datasets[species][group][type_name] = [(dataset_value, dataset_text)] else: - cross2 = cross - cursor.execute("select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %d order by Tissue.Name" % (cross2, webqtlConfig.PUBLICTHRESH)) - typeResults = cursor.fetchall() - typeResultsNum = cursor.rowcount - - if typeResultsNum > 0: - for typeItem in typeResults: - typeVal = typeItem[0] - tIndex = getIndex(searchArray=typeTotalResults, targetValue=typeVal)+1 - # retrieve database(dataset) info based on group(InbredSet) and type(Tissue) - tissue = typeVal - cursor.execute("select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name in ('%s') and Tissue.name = '%s' and ProbeSetFreeze.public > %d order by ProbeSetFreeze.CreateTime desc" % (cross2, tissue, webqtlConfig.PUBLICTHRESH)) - datasetResults = cursor.fetchall() - datasetResultsNum = cursor.rowcount - - if datasetResultsNum > 0: - for datasetItem in datasetResults: - datasetVal = datasetItem[0] - dIndex = getIndex(searchArray=datasetTotalResults, targetValue=datasetVal)+1 - outputLinkStr +='[%d,%d,%d,%d],\n'%(sIndex,gIndex,tIndex,dIndex) - -# add 'All Phenotypes' option for 'Database' select menu -# for 'All Species'option in 'Species' select menu, 'Database' select menu will show 'All Phenotypes' option -outputDatabaseStr += '{txt:\'%s\',val:\'%s\'}];\n\n'%('All Phenotypes','_allPublish') -datasetTotalResults.append(('_allPublish','All Phenotypes')) - -sIndex = getIndex(searchArray=speciesTotalResult,targetValue='All Species')+1 -gIndex = getIndex(searchArray=groupTotalResults, targetValue='all groups')+1 -tIndex = getIndex(searchArray=typeTotalResults,targetValue='Phenotypes')+1 -dIndex = getIndex(searchArray=datasetTotalResults, targetValue='_allPublish')+1 -outputLinkStr +='[%d,%d,%d,%d]];\n\n'%(sIndex,gIndex,tIndex,dIndex) - -# Combine sArr, gArr, tArr, dArr and lArr output string together -outputStr = outputTimeStr+outputSpeciesStr+outputGroupStr+outputTypeStr+outputDatabaseStr+outputLinkStr -outputStr +=''' - -/* -* function: based on different browser use, will have different initial actions; -* Once the index.html page is loaded, this function will be called -*/ -function initialDatasetSelection() -{ - defaultSpecies =getDefaultValue('species'); - defaultSet =getDefaultValue('cross'); - defaultType =getDefaultValue('tissue'); - defaultDB =getDefaultValue('database'); - - if (navigator.userAgent.indexOf('MSIE')>=0) - { - sOptions = fillOptionsForIE(null,defaultSpecies); - var menu0 =""; - document.getElementById('menu0').innerHTML = menu0; - - gOptions = fillOptionsForIE('species',defaultSet); - var menu1 =""; - document.getElementById('menu1').innerHTML =menu1; - - tOptions = fillOptionsForIE('cross',defaultType); - var menu2 =""; - document.getElementById('menu2').innerHTML =menu2; - - dOptions = fillOptionsForIE('tissue',defaultDB); - var menu3 =""; - document.getElementById('menu3').innerHTML =menu3; - - }else{ - fillOptions(null); - } - searchtip(); -} - -/* -* input: selectObjId (designated select menu, such as species, cross, etc... ) -* defaultValue (default Value of species, cross,tissue or database) -* function: special for IE browser,setting options value for select menu dynamically based on linkage array(lArr), -* output: options string -*/ -function fillOptionsForIE(selectObjId,defaultValue) -{ - var options=''; - if(selectObjId==null) - { - var len = sArr.length; - for (var i=1; i < len; i++) { - // setting Species' option - if( sArr[i].val==defaultValue){ - options =options+""; - }else{ - options =options+""; - } - } - }else if(selectObjId=='species') - { - var speciesObj = document.getElementById('species'); - var len = lArr.length; - var arr = []; - var idx = 0; - for (var i=1; i < len; i++) { - //get group(cross) info from lArr - if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1])) - { - arr[idx++]=lArr[i][1]; - } - } - idx=0; - len = arr.length; - removeOptions("cross"); - for (var i=0; i < len; i++) { - // setting Group's option - if( gArr[arr[i]].val==defaultValue){ - options =options+""; - }else{ - options =options+""; - } - - } - }else if(selectObjId=='cross') - { - var speciesObj = document.getElementById('species'); - var groupObj = document.getElementById('cross'); - var len = lArr.length; - var arr = []; - var idx = 0; - for (var i=1; i < len; i++) { - //get type(tissue) info from lArr - if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2])) - { - arr[idx++]=lArr[i][2]; - } - } - idx=0; - len = arr.length; - removeOptions("tissue"); - for (var i=0; i < len; i++) { - // setting Type's option - if( tArr[arr[i]].val==defaultValue){ - options =options+""; - }else{ - options =options+""; - } - } - - }else if(selectObjId=='tissue') - { - var speciesObj = document.getElementById('species'); - var groupObj = document.getElementById('cross'); - var typeObj = document.getElementById('tissue'); - - var len = lArr.length; - var arr = []; - var idx = 0; - for (var i=1; i < len; i++) { - //get dataset(database) info from lArr - if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3])) - { - arr[idx++]=lArr[i][3]; - } - } - idx=0; - len = arr.length; - removeOptions("database"); - for (var i=0; i < len; i++) { - // setting Database's option - if( dArr[arr[i]].val==defaultValue){ - options =options+""; - }else{ - options =options+""; - } - } - } - return options; -} -/* -* input: selectObjId (designated select menu, such as species, cross, etc... ) -* function: setting options value for select menu dynamically based on linkage array(lArr) -* output: null -*/ -function fillOptions(selectObjId) -{ - if(selectObjId==null) - { - - var speciesObj = document.getElementById('species'); - var len = sArr.length; - for (var i=1; i < len; i++) { - // setting Species' option - speciesObj.options[i-1] = new Option(sArr[i].txt, sArr[i].val); - } - updateChocie('species'); - - }else if(selectObjId=='species') - { - var speciesObj = document.getElementById('species'); - var groupObj = document.getElementById('cross'); - var len = lArr.length; - var arr = []; - var idx = 0; - for (var i=1; i < len; i++) { - //get group(cross) info from lArr - if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&!Contains(arr,lArr[i][1])) - { - arr[idx++]=lArr[i][1]; - } - } - idx=0; - len = arr.length; - removeOptions("cross"); - for (var i=0; i < len; i++) { - // setting Group's option - groupObj.options[idx++] = new Option(gArr[arr[i]].txt, gArr[arr[i]].val); - } - updateChocie('cross'); - - }else if(selectObjId=='cross') - { - var speciesObj = document.getElementById('species'); - var groupObj = document.getElementById('cross'); - var typeObj = document.getElementById('tissue'); - var len = lArr.length; - var arr = []; - var idx = 0; - for (var i=1; i < len; i++) { - //get type(tissue) info from lArr - if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&!Contains(arr,lArr[i][2])) - { - arr[idx++]=lArr[i][2]; - } - } - idx=0; - len = arr.length; - removeOptions("tissue"); - for (var i=0; i < len; i++) { - // setting Type's option - typeObj.options[idx++] = new Option(tArr[arr[i]].txt, tArr[arr[i]].val); - } - updateChocie('tissue'); - - }else if(selectObjId=='tissue') - { - var speciesObj = document.getElementById('species'); - var groupObj = document.getElementById('cross'); - var typeObj = document.getElementById('tissue'); - var databaseObj = document.getElementById('database'); - - var len = lArr.length; - var arr = []; - var idx = 0; - for (var i=1; i < len; i++) { - //get dataset(database) info from lArr - if(lArr[i][0]==(getIndexByValue('species',speciesObj.value)).toString()&&lArr[i][1]==(getIndexByValue('cross',groupObj.value)).toString()&&lArr[i][2]==(getIndexByValue('tissue',typeObj.value)).toString()&&!Contains(arr,lArr[i][3])) - { - arr[idx++]=lArr[i][3]; - } - } - idx=0; - len = arr.length; - removeOptions("database"); - for (var i=0; i < len; i++) { - // setting Database's option - databaseObj.options[idx++] = new Option(dArr[arr[i]].txt, dArr[arr[i]].val); - } - updateChocie('database'); - } -} - -/* -* input: arr (targeted array); obj (targeted value) -* function: check whether targeted array contains targeted value or not -* output: return true, if array contains targeted value, otherwise return false -*/ -function Contains(arr,obj) { - var i = arr.length; - while (i--) { - if (arr[i] == obj) { - return true; - } - } - return false; -} - -/* -* input: selectObj (designated select menu, such as species, cross, etc... ) -* function: clear designated select menu's option -* output: null -*/ -function removeOptions(selectObj) { - if (typeof selectObj != 'object'){ - selectObj = document.getElementById(selectObj); - } - var len = selectObj.options.length; - for (var i=0; i < len; i++) { - // clear current selection - selectObj.options[0] = null; - } -} - -/* -* input: selectObjId (designated select menu, such as species, cross, etc... ) -* Value: target value -* function: retrieve Index info of target value in designated array -* output: index info -*/ -function getIndexByValue(selectObjId,val) -{ - if(selectObjId=='species') - { - for(var i=1;i=0){ - //setting option's selected status - Obj.options[idx].selected=true; - //update the following select menu - fillOptions(objId); - }else{ - Obj.options[0].selected=true; - fillOptions(objId); - } -} - -// setting option's selected status based on default setting or cookie setting for Species, Group, Type and Database select menu in the main search page http://www.genenetwork.org/ -function updateChocie(selectObjId){ - - if (selectObjId =='species') - { - defaultSpecies= getDefaultValue('species'); - //setting option's selected status - setChoice('species',defaultSpecies); - }else if (selectObjId =='cross') - { - defaultSet= getDefaultValue('cross'); - //setting option's selected status - setChoice('cross',defaultSet); - }else if (selectObjId =='tissue') - { - defaultType= getDefaultValue('tissue'); - //setting option's selected status - setChoice('tissue',defaultType); - }else if (selectObjId =='database') - { - defaultDB= getDefaultValue('database'); - //setting option's selected status - setChoice('database',defaultDB); - } -} - -//get default value;if cookie exists, then use cookie value, otherwise use default value -function getDefaultValue(selectObjId){ - //define default value - var defaultSpecies = 'mouse' - var defaultSet = 'BXD' - var defaultType = 'Hippocampus' - var defaultDB = 'HC_M2_0606_P' - - if (selectObjId =='species') - { - //if cookie exists, then use cookie value, otherwise use default value - var cookieSpecies = getCookie('defaultSpecies'); - if(cookieSpecies) - { - defaultSpecies= cookieSpecies; - } - return defaultSpecies; - }else if (selectObjId =='cross'){ - var cookieSet = getCookie('defaultSet'); - if(cookieSet){ - defaultSet= cookieSet; - } - return defaultSet; - }else if (selectObjId =='tissue'){ - var cookieType = getCookie('defaultType'); - if(cookieType){ - defaultType= cookieType; - } - return defaultType; - }else if (selectObjId =='database') - { - var cookieDB = getCookie('defaultDB'); - if(cookieDB){ - defaultDB= cookieDB; - } - return defaultDB; - } - -} - -//setting default value into cookies for the dropdown menus: Species,Group, Type, and Database -function setDefault(thisform){ - - setCookie('cookieTest', 'cookieTest', 1); - var cookieTest = getCookie('cookieTest'); - delCookie('cookieTest'); - if (cookieTest){ - var defaultSpecies = thisform.species.value; - setCookie('defaultSpecies', defaultSpecies, 10); - var defaultSet = thisform.cross.value; - setCookie('defaultSet', defaultSet, 10); - var defaultType = thisform.tissue.value; - setCookie('defaultType', defaultType, 10); - var defaultDB = thisform.database.value; - setCookie('defaultDB', defaultDB, 10); - updateChocie('species'); - updateChocie('cross'); - updateChocie('tissue'); - updateChocie('database'); - alert("The current settings are now your default"); - } - else{ - alert("You need to enable Cookies in your browser."); - } -} - -''' -# write all strings' info into selectDatasetMenu.js file -fileHandler.write(outputStr) -fileHandler.close() + Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from + ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s + and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = + InbredSet.Id and ProbeSetFreeze.public > %s order by + ProbeSetFreeze.CreateTime desc""", (type_name, + webqtlConfig.PUBLICTHRESH)) + datasets[species][group][type_name] = Cursor.fetchall() + + return datasets + + +def main(): + species = get_species() + groups = get_groups(species) + types = get_types(groups) + datasets = get_datasets(types) + + species.append(('All Species', 'All Species')) + groups['All Species'] = [('All Groups', 'All Groups')] + types['All Species'] = {} + types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')] + datasets['All Species'] = {} + datasets['All Species']['All Groups'] = {} + datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')] + + data = dict(species=species, + groups=groups, + types=types, + datasets=datasets, + ) + + output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" + + with open(output_file, 'w') as fh: + json.dump(data, fh, indent=" ", sort_keys=True) + + +if __name__ == '__main__': + main() \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json new file mode 100644 index 00000000..d25d3cf5 --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -0,0 +1,6792 @@ +{ + "datasets": { + "All Species": { + "All Groups": { + "Phenotypes": [ + [ + "All Phenotypes", + "All Phenotypes" + ] + ] + } + }, + "arabidopsis": { + "BayXSha": { + "Genotypes": [ + [ + "BayXShaGeno", + "BayXSha Genotypes" + ] + ], + "Phenotypes": [ + [ + "BayXShaPublish", + "BayXSha Published Phenotypes" + ] + ] + }, + "ColXBur": { + "Genotypes": [ + [ + "ColXBurGeno", + "ColXBur Genotypes" + ] + ], + "Phenotypes": [ + [ + "ColXBurPublish", + "ColXBur Published Phenotypes" + ] + ] + }, + "ColXCvi": { + "Genotypes": [ + [ + "ColXCviGeno", + "ColXCvi Genotypes" + ] + ], + "Phenotypes": [ + [ + "ColXCviPublish", + "ColXCvi Published Phenotypes" + ] + ] + } + }, + "barley": { + "QSM": { + "Genotypes": [ + [ + "QSMGeno", + "QSM Genotypes" + ] + ], + "Leaf": [ + [ + "B1LI0809R", + "Barley1 Leaf INOC TTKS (Aug09) RMA" + ], + [ + "B1LI0809M5", + "Barley1 Leaf INOC TTKS (Aug09) MAS5" + ], + [ + "B1MI0809M5", + "Barley1 Leaf MOCK TTKS (Aug09) MAS5" + ], + [ + "B1MI0809R", + "Barley1 Leaf MOCK TTKS (Aug09) RMA" + ], + [ + "B30_K_1206_M", + "Barley1 Leaf MAS 5.0 SCRI (Dec06)" + ], + [ + "B30_K_1206_R", + "Barley1 Leaf gcRMA SCRI (Dec06)" + ], + [ + "B30_K_1206_Rn", + "Barley1 Leaf gcRMAn SCRI (Dec06)" + ] + ], + "Phenotypes": [ + [ + "QSMPublish", + "QSM Published Phenotypes" + ] + ] + }, + "SXM": { + "Embryo": [ + [ + "B139_K_1206_R", + "Barley1 Embryo gcRMA SCRI (Dec06)" + ], + [ + "B139_K_1206_M", + "Barley1 Embryo MAS 5.0 SCRI (Dec06)" + ], + [ + "B150_K_0406_R", + "Barley1 Embryo0 gcRMA SCRI (Apr06)" + ] + ], + "Genotypes": [ + [ + "SXMGeno", + "SXM Genotypes" + ] + ], + "Leaf": [ + [ + "B1LI0809R", + "Barley1 Leaf INOC TTKS (Aug09) RMA" + ], + [ + "B1LI0809M5", + "Barley1 Leaf INOC TTKS (Aug09) MAS5" + ], + [ + "B1MI0809M5", + "Barley1 Leaf MOCK TTKS (Aug09) MAS5" + ], + [ + "B1MI0809R", + "Barley1 Leaf MOCK TTKS (Aug09) RMA" + ], + [ + "B30_K_1206_M", + "Barley1 Leaf MAS 5.0 SCRI (Dec06)" + ], + [ + "B30_K_1206_R", + "Barley1 Leaf gcRMA SCRI (Dec06)" + ], + [ + "B30_K_1206_Rn", + "Barley1 Leaf gcRMAn SCRI (Dec06)" + ] + ], + "Phenotypes": [ + [ + "SXMPublish", + "SXM Published Phenotypes" + ] + ] + } + }, + "drosophila": { + "DGRP": { + "Genotypes": [ + [ + "DGRPGeno", + "DGRP Genotypes" + ] + ], + "Phenotypes": [ + [ + "DGRPPublish", + "DGRP Published Phenotypes" + ] + ], + "Whole Body": [ + [ + "NCSU_DrosWB_LC_RMA_0111", + "NCSU Drosophila Whole Body (Jan11) RMA" + ], + [ + "UAB_DrosWB_LC_RMA_1009", + "UAB Whole body D.m. mRNA control (Oct09) RMA" + ], + [ + "UAB_DrosWB_LE_RMA_1009", + "UAB Whole body D.m. mRNA lead (pbAc) (Oct09) RMA" + ] + ] + }, + "Oregon-R_x_2b3": { + "Genotypes": [ + [ + "Oregon-R_x_2b3Geno", + "Oregon-R_x_2b3 Genotypes" + ] + ], + "Phenotypes": [ + [ + "Oregon-R_x_2b3Publish", + "Oregon-R_x_2b3 Published Phenotypes" + ] + ], + "Whole Body": [ + [ + "NCSU_DrosWB_LC_RMA_0111", + "NCSU Drosophila Whole Body (Jan11) RMA" + ], + [ + "UAB_DrosWB_LC_RMA_1009", + "UAB Whole body D.m. mRNA control (Oct09) RMA" + ], + [ + "UAB_DrosWB_LE_RMA_1009", + "UAB Whole body D.m. mRNA lead (pbAc) (Oct09) RMA" + ] + ] + } + }, + "human": { + "AD-cases-controls": { + "Brain": [ + [ + "GSE15222_F_N_RI_0409", + "GSE15222 Human Brain Normal Myers (Apr09) RankInv" + ], + [ + "GSE15222_F_A_RI_0409", + "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" + ], + [ + "GSE5281_F_RMA_N_0709", + "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" + ], + [ + "GSE5281_F_RMA_Alzh_0709", + "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" + ], + [ + "INIA_MacFas_brain_RMA_0110", + "INIA Macaca fasicularis Brain (Jan10) RMA **" + ], + [ + "GSE15222_F_RI_0409", + "GSE15222 Human Brain Myers (Apr09) RankInv" + ], + [ + "GSE5281_F_RMA0709", + "GSE5281 Human Brain Full Liang (Jul09) RMA" + ], + [ + "GSE5281_RMA0709", + "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" + ], + [ + "UCLA_CTB6B6CTF2_BRAIN_FEMALE", + "UCLA CTB6B6CTF2 Brain Female mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_BRAIN_MALE", + "UCLA CTB6B6CTF2 Brain Male mlratio **" + ], + [ + "UCLA_BHF2_BRAIN_MALE", + "UCLA BHF2 Brain Male mlratio" + ], + [ + "UCLA_BHF2_BRAIN_FEMALE", + "UCLA BHF2 Brain Female mlratio" + ], + [ + "UCLA_BHHBF2_BRAIN_FEMALE", + "UCLA BHHBF2 Brain Female Only" + ], + [ + "UCLA_BHHBF2_BRAIN_MALE", + "UCLA BHHBF2 Brain Male Only" + ], + [ + "UCLA_BHHBF2_BRAIN_2005", + "UCLA BHHBF2 Brain (2005) mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_BRAIN_2005", + "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" + ], + [ + "UCLA_BHF2_BRAIN_0605", + "UCLA BHF2 Brain (June05) mlratio" + ], + [ + "BR_M2_1106_R", + "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" + ], + [ + "IBR_M_0606_R", + "INIA Brain mRNA M430 (Jun06) RMA" + ], + [ + "IBR_M_0106_P", + "INIA Brain mRNA M430 (Jan06) PDNN" + ], + [ + "IBR_M_0106_R", + "INIA Brain mRNA M430 (Jan06) RMA" + ], + [ + "BR_U_1105_P", + "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" + ], + [ + "BR_U_0805_M", + "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" + ], + [ + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], + [ + "BR_U_0805_R", + "UTHSC Brain mRNA U74Av2 (Aug05) RMA" + ], + [ + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + ], + [ + "BRF2_M_0805_P", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" + ], + [ + "BRF2_M_0805_M", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" + ], + [ + "BRF2_M_0304_P", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" + ], + [ + "BRF2_M_0304_R", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" + ], + [ + "BRF2_M_0304_M", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" + ], + [ + "CB_M_0204_P", + "INIA Brain mRNA M430 (Feb04) PDNN" + ] + ], + "Genotypes": [ + [ + "AD-cases-controlsGeno", + "AD-cases-controls Genotypes" + ] + ], + "Phenotypes": [ + [ + "AD-cases-controlsPublish", + "AD-cases-controls Published Phenotypes" + ] + ] + }, + "AD-cases-controls-Myers": { + "Brain": [ + [ + "GSE15222_F_N_RI_0409", + "GSE15222 Human Brain Normal Myers (Apr09) RankInv" + ], + [ + "GSE15222_F_A_RI_0409", + "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" + ], + [ + "GSE5281_F_RMA_N_0709", + "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" + ], + [ + "GSE5281_F_RMA_Alzh_0709", + "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" + ], + [ + "INIA_MacFas_brain_RMA_0110", + "INIA Macaca fasicularis Brain (Jan10) RMA **" + ], + [ + "GSE15222_F_RI_0409", + "GSE15222 Human Brain Myers (Apr09) RankInv" + ], + [ + "GSE5281_F_RMA0709", + "GSE5281 Human Brain Full Liang (Jul09) RMA" + ], + [ + "GSE5281_RMA0709", + "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" + ], + [ + "UCLA_CTB6B6CTF2_BRAIN_FEMALE", + "UCLA CTB6B6CTF2 Brain Female mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_BRAIN_MALE", + "UCLA CTB6B6CTF2 Brain Male mlratio **" + ], + [ + "UCLA_BHF2_BRAIN_MALE", + "UCLA BHF2 Brain Male mlratio" + ], + [ + "UCLA_BHF2_BRAIN_FEMALE", + "UCLA BHF2 Brain Female mlratio" + ], + [ + "UCLA_BHHBF2_BRAIN_FEMALE", + "UCLA BHHBF2 Brain Female Only" + ], + [ + "UCLA_BHHBF2_BRAIN_MALE", + "UCLA BHHBF2 Brain Male Only" + ], + [ + "UCLA_BHHBF2_BRAIN_2005", + "UCLA BHHBF2 Brain (2005) mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_BRAIN_2005", + "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" + ], + [ + "UCLA_BHF2_BRAIN_0605", + "UCLA BHF2 Brain (June05) mlratio" + ], + [ + "BR_M2_1106_R", + "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" + ], + [ + "IBR_M_0606_R", + "INIA Brain mRNA M430 (Jun06) RMA" + ], + [ + "IBR_M_0106_P", + "INIA Brain mRNA M430 (Jan06) PDNN" + ], + [ + "IBR_M_0106_R", + "INIA Brain mRNA M430 (Jan06) RMA" + ], + [ + "BR_U_1105_P", + "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" + ], + [ + "BR_U_0805_M", + "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" + ], + [ + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" + ], + [ + "BR_U_0805_R", + "UTHSC Brain mRNA U74Av2 (Aug05) RMA" + ], + [ + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + ], + [ + "BRF2_M_0805_P", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" + ], + [ + "BRF2_M_0805_M", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" + ], + [ + "BRF2_M_0304_P", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" + ], + [ + "BRF2_M_0304_R", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" + ], + [ + "BRF2_M_0304_M", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" + ], + [ + "CB_M_0204_P", + "INIA Brain mRNA M430 (Feb04) PDNN" + ] + ], + "Genotypes": [ + [ + "AD-cases-controls-MyersGeno", + "AD-cases-controls-Myers Genotypes" + ] + ], + "Phenotypes": [ + [ + "AD-cases-controls-MyersPublish", + "AD-cases-controls-Myers Published Phenotypes" + ] + ] + }, + "CANDLE": { + "Genotypes": [ + [ + "CANDLEGeno", + "CANDLE Genotypes" + ] + ], + "Newborn Cord Blood": [ + [ + "CANDLE_NB_0711", + "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT **" + ] + ], + "Phenotypes": [ + [ + "CANDLEPublish", + "CANDLE Published Phenotypes" + ] + ] + }, + "CEPH-2004": { + "Genotypes": [ + [ + "CEPH-2004Geno", + "CEPH-2004 Genotypes" + ] + ], + "Lymphoblast B-cell": [ + [ + "UT_CEPH_RankInv0909", + "UTHSC CEPH B-cells Illumina (Sep09) RankInv" + ], + [ + "Human_1008", + "Monks CEPH B-cells Agilent (Dec04) Log10Ratio" + ] + ], + "Phenotypes": [ + [ + "CEPH-2004Publish", + "CEPH-2004 Published Phenotypes" + ] + ] + }, + "HB": { + "Cerebellum": [ + [ + "HBTRC-MLC_0611", + "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + ], + [ + "HBTRC-MLC_N_0611", + "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + ], + [ + "HBTRC-MLC_AD_0611", + "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + ], + [ + "HBTRC-MLC_HD_0611", + "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + ], + [ + "GCB_M2_0505_M", + "GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5" + ], + [ + "GCB_M2_0505_R", + "GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA" + ], + [ + "GCB_M2_0505_P", + "GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN" + ], + [ + "CB_M_0305_R", + "SJUT Cerebellum mRNA M430 (Mar05) RMA" + ], + [ + "CB_M_0305_M", + "SJUT Cerebellum mRNA M430 (Mar05) MAS5" + ], + [ + "CB_M_0305_P", + "SJUT Cerebellum mRNA M430 (Mar05) PDNN" + ], + [ + "CB_M_1004_R", + "SJUT Cerebellum mRNA M430 (Oct04) RMA" + ], + [ + "CB_M_1004_M", + "SJUT Cerebellum mRNA M430 (Oct04) MAS5" + ], + [ + "CB_M_1004_P", + "SJUT Cerebellum mRNA M430 (Oct04) PDNN" + ], + [ + "CB_M_1003_M", + "SJUT Cerebellum mRNA M430 (Oct03) MAS5" + ] + ], + "Genotypes": [ + [ + "HBGeno", + "HB Genotypes" + ] + ], + "Phenotypes": [ + [ + "HBPublish", + "HB Published Phenotypes" + ] + ], + "Prefrontal Cortex": [ + [ + "HBTRC-MLPFC_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + ], + [ + "HBTRC-MLPFC_N_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "HBTRC-MLPFC_AD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + ], + [ + "HBTRC-MLPFC_HD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + ], + [ + "INIA_MacFas_Pf_RMA_0110", + "INIA Macaca fasicularis Prefrontal Cortex control (Jan10) RMA **" + ], + [ + "INIA_MacFas_PfE_RMA_0110", + "INIA Macaca fasicularis Prefrontal Cortex ethanol (Jan10) RMA **" + ], + [ + "VCUSal_1006_R", + "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + ], + [ + "VCUEtOH_1206_R", + "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" + ], + [ + "VCUSal_1206_R", + "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" + ], + [ + "VCU_PF_Air_0111_R", + "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" + ], + [ + "VCU_PF_Et_0111_R", + "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **" + ], + [ + "VCU_PF_AvE_0111_Ss", + "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" + ], + [ + "VCUEt_vs_Sal_0806_R", + "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" + ], + [ + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" + ], + [ + "VCUSal_0806_R", + "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" + ] + ], + "Primary Visual Cortex": [ + [ + "KIN_YSM_V1C_0711", + "KIN/YSM Human V1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ], + [ + "HBTRC-MLVC_0611", + "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" + ], + [ + "HBTRC-MLVC_N_0611", + "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" + ], + [ + "HBTRC-MLVC_AD_0611", + "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" + ], + [ + "HBTRC-MLVC_HD_0611", + "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + ] + ] + }, + "HLC": { + "Genotypes": [ + [ + "HLCGeno", + "HLC Genotypes" + ] + ], + "Liver": [ + [ + "GSE16780_UCLA_ML0911", + "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" + ], + [ + "JAX_CSB_L_0711", + "JAX Liver Affy M430 2.0 (Jul11) MDP" + ], + [ + "JAX_CSB_L_HF_0711", + "JAX Liver HF Affy M430 2.0 (Jul11) MDP" + ], + [ + "JAX_CSB_L_6C_0711", + "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" + ], + [ + "HLC_0311", + "GSE9588 Human Liver Normal (Mar11) Both Sexes" + ], + [ + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" + ], + [ + "LV_G_0106_F", + "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" + ], + [ + "LV_G_0106_M", + "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" + ], + [ + "LV_G_0106_B", + "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" + ], + [ + "GenEx_BXD_liverSal_RMA_F_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" + ], + [ + "GenEx_BXD_liverSal_RMA_M_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" + ], + [ + "GenEx_BXD_liverSal_RMA_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + ], + [ + "GenEx_BXD_liverEt_RMA_F_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" + ], + [ + "GenEx_BXD_liverEt_RMA_M_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" + ], + [ + "GenEx_BXD_liverEt_RMA_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + ], + [ + "SUH_Liv_RMA_0611", + "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" + ], + [ + "OXUKHS_ILMLiver_RI0510", + "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" + ], + [ + "HXB_Liver_1208", + "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_MALE", + "UCLA CTB6B6CTF2 Liver Male mlratio **" + ], + [ + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male mlratio" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_FEMALE", + "UCLA CTB6B6CTF2 Liver Female mlratio **" + ], + [ + "UCLA_BHHBF2_LIVER_FEMALE", + "UCLA BHHBF2 Liver Female Only" + ], + [ + "UCLA_BHHBF2_LIVER_MALE", + "UCLA BHHBF2 Liver Male Only" + ], + [ + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], + [ + "UCLA_BHHBF2_LIVER_2005", + "UCLA BHHBF2 Liver (2005) mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_2005", + "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" + ], + [ + "UCLA_BHF2_LIVER_0605", + "UCLA BHF2 Liver (June05) mlratio" + ], + [ + "UCLA_BDF2_LIVER_1999", + "UCLA BDF2 Liver (1999) mlratio" + ], + [ + "LVF2_M_0704_R", + "(B6 x BTBR)F2-ob/ob Liver 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[ + "UCLA_BHHBF2_LIVER_MALE", + "UCLA BHHBF2 Liver Male Only" + ], + [ + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], + [ + "UCLA_BHHBF2_LIVER_2005", + "UCLA BHHBF2 Liver (2005) mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_2005", + "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" + ], + [ + "UCLA_BHF2_LIVER_0605", + "UCLA BHF2 Liver (June05) mlratio" + ], + [ + "UCLA_BDF2_LIVER_1999", + "UCLA BDF2 Liver (1999) mlratio" + ], + [ + "LVF2_M_0704_R", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" + ], + [ + "LVF2_M_0704_M", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" + ], + [ + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" + ] + ], + "Muscle": [ + [ + "EPFLMouseMuscleRMA1211", + "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + ], + [ + "EPFLMouseMuscleCDRMA1211", + "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + ], + [ + "EPFLMouseMuscleHFDRMA1211", + "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" 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], + [ + "UCLA_BHHBF2_LIVER_MALE", + "UCLA BHHBF2 Liver Male Only" + ], + [ + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], + [ + "UCLA_BHHBF2_LIVER_2005", + "UCLA BHHBF2 Liver (2005) mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_2005", + "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" + ], + [ + "UCLA_BHF2_LIVER_0605", + "UCLA BHF2 Liver (June05) mlratio" + ], + [ + "UCLA_BDF2_LIVER_1999", + "UCLA BDF2 Liver (1999) mlratio" + ], + [ + "LVF2_M_0704_R", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" + ], + [ + "LVF2_M_0704_M", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" + ], + [ + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" + ] + ], + "Muscle": [ + [ + "EPFLMouseMuscleRMA1211", + "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + ], + [ + "EPFLMouseMuscleCDRMA1211", + "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + ], + [ + "EPFLMouseMuscleHFDRMA1211", + "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) 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"UCLA_BXDBXH_CARTILAGE_V2", + "UCLA BXD and BXH Cartilage v2" + ], + [ + "UCLA_BXHBXD_CARTILAGE_V2", + "UCLA BXH and BXD Cartilage v2" + ], + [ + "UCLA_BXDBXH_CARTILAGE", + "UCLA BXD and BXH Cartilage" + ], + [ + "UCLA_BXHBXD_CARTILAGE", + "UCLA BXH and BXD Cartilage" + ], + [ + "UCLA_BXD_CARTILAGE", + "UCLA BXD Cartilage" + ], + [ + "UCLA_BXH_CARTILAGE", + "UCLA BXH Cartilage" + ] + ], + "Cerebellum": [ + [ + "HBTRC-MLC_0611", + "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" + ], + [ + "HBTRC-MLC_N_0611", + "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" + ], + [ + "HBTRC-MLC_AD_0611", + "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" + ], + [ + "HBTRC-MLC_HD_0611", + "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" + ], + [ + "GCB_M2_0505_M", + "GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5" + ], + [ + "GCB_M2_0505_R", + "GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA" + ], + [ + "GCB_M2_0505_P", + "GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN" + ], + [ + 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"KIN_YSM_HIP_0711", + "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ], + [ + "UMUTAffyExon_0209_RMA_MDP", + "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "HC_M2_0606_MDP", + "Hippocampus Consortium M430v2 (Jun06) RMA MDP" + ], + [ + "OXUKHS_ILMHipp_RI0510", + "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" + ], + [ + "INIA_MacFas_Hc_RMA_0110", + "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" + ], + [ + "INIA_MacFas_He_RMA_0110", + "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" + ], + [ + "UT_HippRatEx_RMA_0709", + "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" + ], + [ + "Illum_LXS_Hipp_loess0807", + "Hippocampus Illumina (Aug07) LOESS" + ], + [ + "Illum_LXS_Hipp_loess_nb0807", + "Hippocampus Illumina (Aug07) LOESS_NB" + ], + [ + "Illum_LXS_Hipp_quant0807", + "Hippocampus Illumina (Aug07) QUANT" + ], + [ + "Illum_LXS_Hipp_quant_nb0807", + "Hippocampus Illumina (Aug07) QUANT_NB" + ], + [ + "Illum_LXS_Hipp_rsn0807", + "Hippocampus 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Mouse Gene 1.0 ST (Jun11) RMA **" + ], + [ + "OXUKHS_ILMLiver_RI0510", + "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" + ], + [ + "HXB_Liver_1208", + "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_MALE", + "UCLA CTB6B6CTF2 Liver Male mlratio **" + ], + [ + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male mlratio" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_FEMALE", + "UCLA CTB6B6CTF2 Liver Female mlratio **" + ], + [ + "UCLA_BHHBF2_LIVER_FEMALE", + "UCLA BHHBF2 Liver Female Only" + ], + [ + "UCLA_BHHBF2_LIVER_MALE", + "UCLA BHHBF2 Liver Male Only" + ], + [ + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" + ], + [ + "UCLA_BHHBF2_LIVER_2005", + "UCLA BHHBF2 Liver (2005) mlratio **" + ], + [ + "UCLA_CTB6B6CTF2_LIVER_2005", + "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" + ], + [ + "UCLA_BHF2_LIVER_0605", + "UCLA BHF2 Liver (June05) mlratio" + ], + [ + "UCLA_BDF2_LIVER_1999", + "UCLA BDF2 Liver (1999) mlratio" + ], + [ + "LVF2_M_0704_R", + "(B6 x BTBR)F2-ob/ob Liver 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"Genotypes" + ], + [ + "Mammary Tumors", + "Mammary Tumors mRNA" + ] + ], + "AXBXA": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Eye", + "Eye mRNA" + ] + ], + "B6BTBRF2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Liver", + "Liver mRNA" + ] + ], + "B6D2F2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Brain", + "Brain mRNA" + ] + ], + "BDF2-1999": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Liver", + "Liver mRNA" + ] + ], + "BDF2-2005": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Striatum", + "Striatum mRNA" + ] + ], + "BHF2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Adipose", + "Adipose mRNA" + ], + [ + "Brain", + "Brain mRNA" + ], + [ + "Liver", + "Liver mRNA" + ], + [ + "Muscle", + "Muscle mRNA" + ] + ], + "BHHBF2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Adipose", + "Adipose mRNA" + ], + [ + "Brain", + "Brain mRNA" + ], + [ + "Liver", + "Liver mRNA" + ], + [ + "Muscle", + "Muscle mRNA" + ] + ], + "BXD": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Amygdala", + "Amygdala mRNA" + ], + [ + "Brain", + "Brain mRNA" + ], + [ + "Cartilage", + "Cartilage mRNA" + ], + [ + "Cerebellum", + "Cerebellum mRNA" + ], + [ + "Eye", + "Eye mRNA" + ], + [ + "Hematopoietic Cells", + "Hematopoietic Cells mRNA" + ], + [ + "Hippocampus", + "Hippocampus mRNA" + ], + [ + "Hypothalamus", + "Hypothalamus mRNA" + ], + [ + "Kidney", + "Kidney mRNA" + ], + [ + "Leucocytes", + "Leucocytes mRNA" + ], + [ + "Liver", + "Liver mRNA" + ], + [ + "Lung", + "Lung mRNA" + ], + [ + "Midbrain", + "Midbrain mRNA" + ], + [ + "Muscle", + "Muscle mRNA" + ], + [ + "Neocortex", + "Neocortex mRNA" + ], + [ + "Nucleus Accumbens", + "Nucleus Accumbens mRNA" + ], + [ + "Prefrontal Cortex", + "Prefrontal Cortex mRNA" + ], + [ + "Retina", + "Retina mRNA" + ], + [ + "Spleen", + "Spleen mRNA" + ], + [ + "Striatum", + "Striatum mRNA" + ], + [ + "T Cell (helper)", + "T Cell (helper) mRNA" + ], + [ + "T Cell (regulatory)", + "T Cell (regulatory) mRNA" + ], + [ + "Thymus", + "Thymus mRNA" + ], + [ + "Ventral Tegmental Area", + "Ventral Tegmental Area mRNA" + ] + ], + "BXH": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Cartilage", + "Cartilage mRNA" + ] + ], + "CTB6F2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Adipose", + "Adipose mRNA" + ], + [ + "Brain", + "Brain mRNA" + ], + [ + "Liver", + "Liver mRNA" + ], + [ + "Muscle", + "Muscle mRNA" + ] + ], + "CXB": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Hippocampus", + "Hippocampus mRNA" + ], + [ + "Spleen", + "Spleen mRNA" + ] + ], + "HS": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Hippocampus", + "Hippocampus mRNA" + ], + [ + "Liver", + "Liver mRNA" + ], + [ + "Lung", + "Lung mRNA" + ] + ], + "HS-CC": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Striatum", + "Striatum mRNA" + ] + ], + "LXS": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Hippocampus", + "Hippocampus mRNA" + ], + [ + "Prefrontal Cortex", + "Prefrontal Cortex mRNA" + ] + ], + "MDP": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Hippocampus", + "Hippocampus mRNA" + ], + [ + "Liver", + "Liver mRNA" + ] + ], + "NZBXFVB-N2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Mammary Tumors", + "Mammary Tumors mRNA" + ] + ] + }, + "rat": { + "HXBBXH": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Adrenal Gland", + "Adrenal Gland mRNA" + ], + [ + "Heart", + "Heart mRNA" + ], + [ + "Hippocampus", + "Hippocampus mRNA" + ], + [ + "Kidney", + "Kidney mRNA" + ], + [ + "Liver", + "Liver mRNA" + ], + [ + "Peritoneal Fat", + "Peritoneal Fat mRNA" + ] + ], + "SRxSHRSPF2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Eye", + "Eye mRNA" + ] + ] + }, + "soybean": { + "J12XJ58F2": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ] + }, + "tomato": { + "LXP": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ] + } + } +} \ No newline at end of file -- cgit v1.2.3 From 55d78345ba1cd2f56b1aecabf5bb3753bfd7ca13 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Wed, 24 Oct 2012 17:39:43 -0500 Subject: Now builds json datastructure for menus correctly --- wqflask/base/webqtlFormData.py | 57 +- wqflask/maintenance/gen_select_dataset.py | 97 +- wqflask/wqflask/correlation/CorrelationPage.py | 25 +- wqflask/wqflask/search_results.py | 67 +- .../static/new/javascript/dataset_menu_structure | 5984 ++++---------------- wqflask/wqflask/views.py | 9 +- 6 files changed, 1193 insertions(+), 5046 deletions(-) (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index 710c9f53..ff1db0e8 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -44,9 +44,9 @@ from utility import webqtlUtil -class webqtlFormData: +class webqtlFormData(object): 'Represents data from a WebQTL form page, needed to generate the next page' - + attrs = ('formID','RISet','genotype','samplelist','allsamplelist', 'display_variance' 'suggestive','significance','submitID','identification', 'enablevariance', 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') @@ -62,7 +62,7 @@ class webqtlFormData: print("in webqtlFormData start_vars are:", pf(start_vars)) for item in webqtlFormData.attrs: self.__dict__[item] = None - + #ZS: This is only used in DataEditingPage.py (as far as I know) self.varianceDispName = None @@ -103,7 +103,7 @@ class webqtlFormData: self.ppolar = None self.mpolar = None - + print("[yellow] self.RISet is:", self.RISet) if self.RISet: #try: @@ -112,13 +112,13 @@ class webqtlFormData: #except: # f1 = f12 = self.mpolar = self.ppolar = None - + def set_number(stringy): return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000 self.nperm = set_number(self.nperm) self.nboot = set_number(self.nboot) - + #if self.allsamplelist: # self.allsamplelist = map(string.strip, string.split(self.allsamplelist)) @@ -134,6 +134,7 @@ class webqtlFormData: def __getitem__(self, key): + print("in __getitem__") return self.__dict__[key] def get(self, key, default=None): @@ -154,22 +155,22 @@ class webqtlFormData: '''read genotype from .geno file''' if self.RISet == 'BXD300': self.RISet = 'BXD' - + assert self.RISet, "self.RISet needs to be set" - + #genotype_1 is Dataset Object without parents and f1 #genotype_2 is Dataset Object with parents and f1 (not for intercross) - + self.genotype_1 = reaper.Dataset() - + full_filename = os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno') - + # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(full_filename) self.genotype_1.read(full_filename) - + print("Got to after read") - + try: # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] @@ -186,16 +187,16 @@ class webqtlFormData: else: self.incparentsf1 = 0 self.genotype = self.genotype_1 - + self.samplelist = list(self.genotype.prgy) self.f1list = [] self.parlist = [] - + if _f1 and _f12: self.f1list = [_f1, _f12] if _mat and _pat: self.parlist = [_mat, _pat] - + def readData(self, samplelist, incf1=None): '''read user input data or from trait data and analysis form''' @@ -213,11 +214,11 @@ class webqtlFormData: #print("before traitfiledata self.traitfile is:", pf(self.traitfile)) - traitfiledata = getattr(self, "traitfile", None) - traitpastedata = getattr(self, "traitpaste", None) - variancefiledata = getattr(self, "variancefile", None) - variancepastedata = getattr(self, "variancepaste", None) - Nfiledata = getattr(self, "Nfile", None) + traitfiledata = getattr(self, "traitfile", None) + traitpastedata = getattr(self, "traitpaste", None) + variancefiledata = getattr(self, "variancefile", None) + variancepastedata = getattr(self, "variancepaste", None) + Nfiledata = getattr(self, "Nfile", None) #### Todo: Rewrite below when we get to someone submitting their own trait ##### @@ -246,7 +247,7 @@ class webqtlFormData: elif len(values) > len(samplelist): values = values[:len(samplelist)] print("now values is:", values) - + if variancefiledata: tt = variancefiledata.split() @@ -282,16 +283,16 @@ class webqtlFormData: def informativeStrains(self, samplelist=None, include_variances = None): '''if readData was called, use this to output informative samples (sample with values)''' - + if not samplelist: samplelist = self.samplelist - + samples = [] values = [] variances = [] - + #print("self.allTraitData is:", pf(self.allTraitData)) - + for sample in samplelist: if sample in self.allTraitData: _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance @@ -305,13 +306,13 @@ class webqtlFormData: samples.append(sample) values.append(_val) variances.append(None) - + return samples, values, variances, len(samples) #def FormDataAsFloat(self, key): - # + # # #try: # # return float(self.key) # #except: diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 33813051..9224b884 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -76,17 +76,22 @@ def get_types(groups): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code - group = types[species][group_name] = [("Phenotypes", "Phenotypes"), - ("Genotypes", "Genotypes")] - Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from - ProbeFreeze, - ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and + types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")] + types[species][group_name] += build_types(species, group_name) + return types + + +def build_types(species, group): + Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') + from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species + where Species.Name = %s and Species.Id = InbredSet.SpeciesId and + InbredSet.Name = %s and + ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and - InbredSet.Name = %s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.public > %s - order by Tissue.Name""", (group_name, webqtlConfig.PUBLICTHRESH)) - group += Cursor.fetchall() - return types + order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH)) + return Cursor.fetchall() def get_datasets(types): @@ -97,39 +102,44 @@ def get_datasets(types): for group, type_list in group_dict.iteritems(): datasets[species][group] = {} for type_name, type_full_name in type_list: - dataset_text = dataset_value = None - if type_name == "Phenotypes": - dataset_value = "%sPublish" % group - if group == 'MDP': - dataset_text = "Mouse Phenome Database" - else: - dataset_text = "%s Published Phenotypes" % group - - elif type_name == "Genotypes": - dataset_value = "%sGeno" % group - dataset_text = "%s Genotypes" % group - - if dataset_value: - datasets[species][group][type_name] = [(dataset_value, dataset_text)] - else: - Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from - ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s - and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = - InbredSet.Id and ProbeSetFreeze.public > %s order by - ProbeSetFreeze.CreateTime desc""", (type_name, - webqtlConfig.PUBLICTHRESH)) - datasets[species][group][type_name] = Cursor.fetchall() - + datasets[species][group][type_name] = build_datasets(species, group, type_name) return datasets +def build_datasets(species, group, type_name): + dataset_text = dataset_value = None + if type_name == "Phenotypes": + dataset_value = "%sPublish" % group + if group == 'MDP': + dataset_text = "Mouse Phenome Database" + else: + dataset_text = "%s Published Phenotypes" % group + + elif type_name == "Genotypes": + dataset_value = "%sGeno" % group + dataset_text = "%s Genotypes" % group + + if dataset_value: + return [(dataset_value, dataset_text)] + else: + Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from + ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where + Species.Name = %s and Species.Id = InbredSet.SpeciesId and + InbredSet.Name = %s and + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s + and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = + InbredSet.Id and ProbeSetFreeze.public > %s order by + ProbeSetFreeze.CreateTime desc""", ( + species, group, type_name, webqtlConfig.PUBLICTHRESH)) + return Cursor.fetchall() + + def main(): species = get_species() groups = get_groups(species) types = get_types(groups) datasets = get_datasets(types) - + species.append(('All Species', 'All Species')) groups['All Species'] = [('All Groups', 'All Groups')] types['All Species'] = {} @@ -137,18 +147,25 @@ def main(): datasets['All Species'] = {} datasets['All Species']['All Groups'] = {} datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')] - + data = dict(species=species, groups=groups, types=types, datasets=datasets, ) - - output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" - + + output_file = """../wqflask/static/new/javascript/dataset_menu_structure""" + with open(output_file, 'w') as fh: json.dump(data, fh, indent=" ", sort_keys=True) - + + print("\nWrote file to:", output_file) + +def test_it(): + types = build_types("Mouse", "BXD") + print("build_types:", pf(types)) + datasets = build_datasets("Mouse", "BXD", "Hippocampus") + print("build_datasets:", pf(datasets)) if __name__ == '__main__': - main() \ No newline at end of file + main() diff --git a/wqflask/wqflask/correlation/CorrelationPage.py b/wqflask/wqflask/correlation/CorrelationPage.py index a9db493b..e48ea412 100644 --- a/wqflask/wqflask/correlation/CorrelationPage.py +++ b/wqflask/wqflask/correlation/CorrelationPage.py @@ -54,9 +54,6 @@ from dbFunction import webqtlDatabaseFunction import utility.webqtlUtil #this is for parallel computing only. import correlationFunction -import logging -logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO) -_log = logging.getLogger("correlation") METHOD_SAMPLE_PEARSON = "1" METHOD_SAMPLE_RANK = "2" @@ -72,9 +69,9 @@ class AuthException(Exception): pass class Trait(object): - - - def __init__(self, name, raw_values = None, lit_corr = None, tissue_corr = None, p_tissue = None): + + + def __init__(self, name, raw_values = None, lit_corr = None, tissue_corr = None, p_tissue = None): self.name = name self.raw_values = raw_values self.lit_corr = lit_corr @@ -281,12 +278,12 @@ class CorrelationPage(templatePage): def __init__(self, fd): #print("in CorrelationPage __init__ fd is:", pf(fd.__dict__)) # Call the superclass constructor - + # Put everything in fd into self self.__dict__.update(fd.__dict__) - + templatePage.__init__(self, fd) - + #print("in CorrelationPage __init__ now fd is:", pf(fd.__dict__)) # Connect to the database if not self.openMysql(): @@ -298,13 +295,13 @@ class CorrelationPage(templatePage): sample_list = get_sample_data(fd) print("sample_list is", pf(sample_list)) - + # Whether the user chose BXD Only, Non-BXD Only, or All Strains # (replace BXD with whatever the group/inbredset name is) # "mdp" stands for "mouse diversity panel" This is outdated; it now represents any # cases/strains from the non-primary group - mdp_choice = fd.MDPChoice if fd.allstrainlist else None - + mdp_choice = fd.MDPChoice if fd.allstrainlist else None + self.species = get_species(fd, self.cursor) #XZ, 09/18/2008: get all information about the user selected database. @@ -334,11 +331,11 @@ class CorrelationPage(templatePage): if len(self.sample_names) < self.corr_min_informative: detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corr_min_informative, fd.RISet)] self.error(heading=None, detail=detail) - + for key, value in self.__dict__.items(): if key.startswith("corr"): print("[red] %s - %s" % (key, value)) - + #correlation_method = self.CORRELATION_METHODS[self.method] #rankOrder = self.RANK_ORDERS[self.method] diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 585deb8f..d44fbcef 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -36,17 +36,17 @@ from wqflask import parser from utility import webqtlUtil from dbFunction import webqtlDatabaseFunction -import logging -logging.basicConfig(filename=app.config['LOGFILE'], level=logging.INFO) - -_log = logging.getLogger("search") -_ch = logging.StreamHandler() -_log.addHandler(_ch) +#import logging +#logging.basicConfig(filename=app.config['LOGFILE'], level=logging.INFO) +# +#_log = logging.getLogger("search") +#_ch = logging.StreamHandler() +#_log.addHandler(_ch) from utility import formatting import sys -_log.info("sys.path is: %s" % (sys.path)) +#_log.info("sys.path is: %s" % (sys.path)) #from base.JinjaPage import JinjaEnv, JinjaPage @@ -60,20 +60,29 @@ class SearchResultPage(templatePage): nkeywords = 0 def __init__(self, fd): + print("initing SearchResultPage") + import logging_tree + logging_tree.printout() self.fd = fd if not self.openMysql(): - return + print("ge0") + #return + print("ge0.5") + #causeerror + print("type of fd:", type(fd)) self.database = [fd['database']] - + print("ge0.55") if not self.database or self.database == 'spacer': #Error, No database selected heading = "Search Result" detail = ['''No database was selected for this search, please go back and SELECT at least one database.'''] + print("ge0.6") self.error(heading=heading,detail=detail,error="No Database Selected") - return + #return + print("ge1") ########################################### # Names and IDs of RISet / F2 set ########################################### @@ -102,12 +111,12 @@ class SearchResultPage(templatePage): # Can't use paramater substitution for table names apparently db_type = self.database[0].type + "Freeze" print("db_type [%s]: %s" % (type(db_type), db_type)) - + query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type) - + self.cursor.execute(query, (individualDB,)) - + (indId, indName, indFullName, @@ -140,6 +149,7 @@ class SearchResultPage(templatePage): self.error(heading=heading,detail=detail,error="No Database Selected") return + print("ge2") self.database[0].getRISet() self.databaseCrosses = [self.database[0].riset] self.databaseCrossIds = [self.database[0].risetid] @@ -159,6 +169,8 @@ class SearchResultPage(templatePage): detail = ["Search can only be performed among the same type of databases"] self.error(heading=heading,detail=detail,error="Error") return + + print("ge3") if self.dbType == "Publish": self.searchField = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', @@ -182,7 +194,8 @@ class SearchResultPage(templatePage): 'RefSeq_TranscriptId'] elif self.dbType == "Geno": self.searchField = ['Name','Chr'] - + + print("ge4") self.do_search() ########################################### @@ -202,7 +215,7 @@ class SearchResultPage(templatePage): ########################################### # Generate Mysql Query ########################################### - + # Sam: We presume lines below aren't used... #geneIdListQuery = fd.get('geneId', '') #if geneIdListQuery: @@ -346,7 +359,7 @@ class SearchResultPage(templatePage): #self.dict['js1'] = '' #self.dict['js2'] = 'onLoad="pageOffset()"' #self.dict['layer'] = self.generateWarningLayer() - + def start_search(self): pass @@ -674,7 +687,7 @@ class SearchResultPage(templatePage): item = item['search_term'] self.nkeywords += 1 #ZS: If there are both AND and OR keywords, just use the OR keywords - if k >=len(self.ORkeyword2): + if k >=len(self.ORkeyword2): query = self.ANDQuery DescriptionText = self.ANDDescriptionText clausejoin = ' OR ' @@ -763,7 +776,7 @@ class SearchResultPage(templatePage): detail = ["Pattern search is not available for phenotype databases at this time."] self.error(heading=heading,detail=detail,error="Error") return 0 - elif (self.dbType == "ProbeSet" and + elif (self.dbType == "ProbeSet" and ((_2Cmds and reduce(lambda x, y: (y not in [ "MEAN", "LRS", "PVALUE", "TRANSLRS", "CISLRS", "RANGE", "H2" ]) or x, _2Cmds, False))\ @@ -877,29 +890,29 @@ class SearchResultPage(templatePage): query = self.ORQuery DescriptionText = self.ORDescriptionText itemCmd = item[0] - - + + chr_number = item[1] # chromosome number lower_limit = float(item[2]) upper_limit = float(item[3]) - + if self.dbType == "ProbeSet": fname = 'target genes' elif self.dbType == "Geno": fname = 'loci' - + if lower_limit > upper_limit: lower_limit, upper_limit = upper_limit, lower_limit - + clauseItem = " %s.Chr = '%s' and %s.Mb > %2.7f and %s.Mb < %2.7f " % ( self.dbType, chr_number, self.dbType, lower_limit, self.dbType, upper_limit) - - + + query.append(" (%s) " % clauseItem) self.orderByDefalut = itemCmd - - self.results_desc = dict() + + self.results_desc = dict() #DescriptionText.append(HT.Span(' with ', HT.U('target genes'), ' on chromosome %s between %g and %g Mb' % \ # (chr_number, min(lower_limit, upper_limit), max(lower_limit, upper_limit)))) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure b/wqflask/wqflask/static/new/javascript/dataset_menu_structure index d25d3cf5..1b7e4090 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure @@ -78,18 +78,6 @@ [ "B1MI0809R", "Barley1 Leaf MOCK TTKS (Aug09) RMA" - ], - [ - "B30_K_1206_M", - "Barley1 Leaf MAS 5.0 SCRI (Dec06)" - ], - [ - "B30_K_1206_R", - "Barley1 Leaf gcRMA SCRI (Dec06)" - ], - [ - "B30_K_1206_Rn", - "Barley1 Leaf gcRMAn SCRI (Dec06)" ] ], "Phenotypes": [ @@ -121,33 +109,17 @@ ] ], "Leaf": [ - [ - "B1LI0809R", - "Barley1 Leaf INOC TTKS (Aug09) RMA" - ], - [ - "B1LI0809M5", - "Barley1 Leaf INOC TTKS (Aug09) MAS5" - ], - [ - "B1MI0809M5", - "Barley1 Leaf MOCK TTKS (Aug09) MAS5" - ], - [ - "B1MI0809R", - "Barley1 Leaf MOCK TTKS (Aug09) RMA" - ], [ "B30_K_1206_M", "Barley1 Leaf MAS 5.0 SCRI (Dec06)" ], - [ - "B30_K_1206_R", - "Barley1 Leaf gcRMA SCRI (Dec06)" - ], [ "B30_K_1206_Rn", "Barley1 Leaf gcRMAn SCRI (Dec06)" + ], + [ + "B30_K_1206_R", + "Barley1 Leaf gcRMA SCRI (Dec06)" ] ], "Phenotypes": [ @@ -176,14 +148,6 @@ [ "NCSU_DrosWB_LC_RMA_0111", "NCSU Drosophila Whole Body (Jan11) RMA" - ], - [ - "UAB_DrosWB_LC_RMA_1009", - "UAB Whole body D.m. mRNA control (Oct09) RMA" - ], - [ - "UAB_DrosWB_LE_RMA_1009", - "UAB Whole body D.m. mRNA lead (pbAc) (Oct09) RMA" ] ] }, @@ -201,10 +165,6 @@ ] ], "Whole Body": [ - [ - "NCSU_DrosWB_LC_RMA_0111", - "NCSU Drosophila Whole Body (Jan11) RMA" - ], [ "UAB_DrosWB_LC_RMA_1009", "UAB Whole body D.m. mRNA control (Oct09) RMA" @@ -219,14 +179,6 @@ "human": { "AD-cases-controls": { "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], [ "GSE5281_F_RMA_N_0709", "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" @@ -235,14 +187,6 @@ "GSE5281_F_RMA_Alzh_0709", "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" ], - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ], [ "GSE5281_F_RMA0709", "GSE5281 Human Brain Full Liang (Jul09) RMA" @@ -250,4683 +194,881 @@ [ "GSE5281_RMA0709", "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], + ] + ], + "Genotypes": [ [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], + "AD-cases-controlsGeno", + "AD-cases-controls Genotypes" + ] + ], + "Phenotypes": [ [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], + "AD-cases-controlsPublish", + "AD-cases-controls Published Phenotypes" + ] + ] + }, + "AD-cases-controls-Myers": { + "Brain": [ [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" + "GSE15222_F_A_RI_0409", + "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" ], [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" + "GSE15222_F_N_RI_0409", + "GSE15222 Human Brain Normal Myers (Apr09) RankInv" ], [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], + "GSE15222_F_RI_0409", + "GSE15222 Human Brain Myers (Apr09) RankInv" + ] + ], + "Genotypes": [ [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], + "AD-cases-controls-MyersGeno", + "AD-cases-controls-Myers Genotypes" + ] + ], + "Phenotypes": [ [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - ], + "AD-cases-controls-MyersPublish", + "AD-cases-controls-Myers Published Phenotypes" + ] + ] + }, + "CANDLE": { + "Genotypes": [ [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], + "CANDLEGeno", + "CANDLE Genotypes" + ] + ], + "Newborn Cord Blood": [ [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], + "CANDLE_NB_0711", + "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT **" + ] + ], + "Phenotypes": [ [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], + "CANDLEPublish", + "CANDLE Published Phenotypes" + ] + ] + }, + "CEPH-2004": { + "Genotypes": [ [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], + "CEPH-2004Geno", + "CEPH-2004 Genotypes" + ] + ], + "Lymphoblast B-cell": [ [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + "UT_CEPH_RankInv0909", + "UTHSC CEPH B-cells Illumina (Sep09) RankInv" ], [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], + "Human_1008", + "Monks CEPH B-cells Agilent (Dec04) Log10Ratio" + ] + ], + "Phenotypes": [ [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], + "CEPH-2004Publish", + "CEPH-2004 Published Phenotypes" + ] + ] + }, + "HB": { + "Cerebellum": [ [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" + "HBTRC-MLC_0611", + "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" ], [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" + "HBTRC-MLC_N_0611", + "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" ], [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" + "HBTRC-MLC_AD_0611", + "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" ], [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" + "HBTRC-MLC_HD_0611", + "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" ] ], "Genotypes": [ [ - "AD-cases-controlsGeno", - "AD-cases-controls Genotypes" + "HBGeno", + "HB Genotypes" ] ], "Phenotypes": [ [ - "AD-cases-controlsPublish", - "AD-cases-controls Published Phenotypes" + "HBPublish", + "HB Published Phenotypes" ] - ] - }, - "AD-cases-controls-Myers": { - "Brain": [ + ], + "Prefrontal Cortex": [ [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" + "HBTRC-MLPFC_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" ], [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" + "HBTRC-MLPFC_N_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" ], [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" + "HBTRC-MLPFC_AD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" ], [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], + "HBTRC-MLPFC_HD_0611", + "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + ] + ], + "Primary Visual Cortex": [ [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" + "HBTRC-MLVC_0611", + "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" ], [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" + "HBTRC-MLVC_N_0611", + "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" ], [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" + "HBTRC-MLVC_AD_0611", + "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" ], [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], + "HBTRC-MLVC_HD_0611", + "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" + ] + ] + }, + "HLC": { + "Genotypes": [ [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], + "HLCGeno", + "HLC Genotypes" + ] + ], + "Liver": [ [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" + "HLC_0311", + "GSE9588 Human Liver Normal (Mar11) Both Sexes" ], [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" + "HLCM_0311", + "GSE9588 Human Liver Normal (Mar11) Males" ], [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], + "HLCF_0311", + "GSE9588 Human Liver Normal (Mar11) Females" + ] + ], + "Phenotypes": [ [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], + "HLCPublish", + "HLC Published Phenotypes" + ] + ] + }, + "HSB": { + "Amygdala": [ [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], + "KIN_YSM_AMY_0711", + "KIN/YSM Human AMY Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Caudal Ganglionic Eminence": [ [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], + "KIN_YSM_CGE_0711", + "KIN/YSM Human CGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Cerebellar Cortex": [ [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], + "KIN_YSM_CBC_0711", + "KIN/YSM Human CBC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Diencephalon": [ [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ], + "KIN_YSM_DIE_0711", + "KIN/YSM Human DIE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Dorsal Thalamus": [ [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], + "KIN_YSM_DTH_0711", + "KIN/YSM Human DTH Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Dorsolateral Prefrontal Cortex": [ [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], + "KIN_YSM_DFC_0711", + "KIN/YSM Human DFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Frontal Cerebral Wall": [ [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], + "KIN_YSM_FC_0711", + "KIN/YSM Human FC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Genotypes": [ [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - ], + "HSBGeno", + "HSB Genotypes" + ] + ], + "Hippocampus": [ [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], + "KIN_YSM_HIP_0711", + "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Inferior Temporal Cortex": [ [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], + "KIN_YSM_ITC_0711", + "KIN/YSM Human ITC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Lateral Ganglionic Eminence": [ [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], + "KIN_YSM_LGE_0711", + "KIN/YSM Human LGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Medial Ganglionic Eminence": [ [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], + "KIN_YSM_MGE_0711", + "KIN/YSM Human MGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Medial Prefrontal Cortex": [ [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], + "KIN_YSM_MFC_0711", + "KIN/YSM Human MFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Mediodorsal Nucleus of Thalamus": [ [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], + "KIN_YSM_MD_0711", + "KIN/YSM Human MD Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Occipital Cerebral Wall": [ [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], + "KIN_YSM_OC_0711", + "KIN/YSM Human OC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Orbital Prefrontal Cortex": [ [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" - ], + "KIN_YSM_OFC_0711", + "KIN/YSM Human OFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Parietal Cerebral Wall": [ [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" - ], + "KIN_YSM_PC_0711", + "KIN/YSM Human PC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Phenotypes": [ [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], + "HSBPublish", + "HSB Published Phenotypes" + ] + ], + "Posterior Inferior Parietal Cortex": [ [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" + "KIN_YSM_IPC_0711", + "KIN/YSM Human IPC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] ], - "Genotypes": [ + "Posterior Superior Temporal Cortex": [ [ - "AD-cases-controls-MyersGeno", - "AD-cases-controls-Myers Genotypes" + "KIN_YSM_STC_0711", + "KIN/YSM Human STC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] ], - "Phenotypes": [ + "Primary Auditory (A1) Cortex": [ [ - "AD-cases-controls-MyersPublish", - "AD-cases-controls-Myers Published Phenotypes" + "KIN_YSM_A1C_0711", + "KIN/YSM Human A1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] - ] - }, - "CANDLE": { - "Genotypes": [ + ], + "Primary Motor (M1) Cortex": [ [ - "CANDLEGeno", - "CANDLE Genotypes" + "KIN_YSM_M1C_0711", + "KIN/YSM Human M1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] ], - "Newborn Cord Blood": [ + "Primary Somatosensory (S1) Cortex": [ [ - "CANDLE_NB_0711", - "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT **" + "KIN_YSM_S1C_0711", + "KIN/YSM Human S1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] ], - "Phenotypes": [ + "Primary Visual Cortex": [ [ - "CANDLEPublish", - "CANDLE Published Phenotypes" + "KIN_YSM_V1C_0711", + "KIN/YSM Human V1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] - ] - }, - "CEPH-2004": { - "Genotypes": [ + ], + "Striatum": [ [ - "CEPH-2004Geno", - "CEPH-2004 Genotypes" + "KIN_YSM_STR_0711", + "KIN/YSM Human STR Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] ], - "Lymphoblast B-cell": [ + "Temporal Cerebral Wall": [ [ - "UT_CEPH_RankInv0909", - "UTHSC CEPH B-cells Illumina (Sep09) RankInv" - ], + "KIN_YSM_TC_0711", + "KIN/YSM Human TC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + ] + ], + "Upper (Rostral) Rhombic Lip": [ [ - "Human_1008", - "Monks CEPH B-cells Agilent (Dec04) Log10Ratio" + "KIN_YSM_URL_0711", + "KIN/YSM Human URL Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] ], - "Phenotypes": [ + "Ventral Forebrain": [ [ - "CEPH-2004Publish", - "CEPH-2004 Published Phenotypes" + "KIN_YSM_VF_0711", + "KIN/YSM Human VF Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] - ] - }, - "HB": { - "Cerebellum": [ + ], + "Ventrolateral Prefrontal Cortex": [ [ - "HBTRC-MLC_0611", - "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLC_N_0611", - "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLC_AD_0611", - "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLC_HD_0611", - "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" - ], - [ - "GCB_M2_0505_M", - "GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5" - ], - [ - "GCB_M2_0505_R", - "GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA" - ], - [ - "GCB_M2_0505_P", - "GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN" - ], - [ - "CB_M_0305_R", - "SJUT Cerebellum mRNA M430 (Mar05) RMA" - ], - [ - "CB_M_0305_M", - "SJUT Cerebellum mRNA M430 (Mar05) MAS5" - ], - [ - "CB_M_0305_P", - "SJUT Cerebellum mRNA M430 (Mar05) PDNN" - ], - [ - "CB_M_1004_R", - "SJUT Cerebellum mRNA M430 (Oct04) RMA" - ], - [ - "CB_M_1004_M", - "SJUT Cerebellum mRNA M430 (Oct04) MAS5" - ], - [ - "CB_M_1004_P", - "SJUT Cerebellum mRNA M430 (Oct04) PDNN" - ], - [ - "CB_M_1003_M", - "SJUT Cerebellum mRNA M430 (Oct03) MAS5" - ] - ], - "Genotypes": [ - [ - "HBGeno", - "HB Genotypes" - ] - ], - "Phenotypes": [ - [ - "HBPublish", - "HB Published Phenotypes" - ] - ], - "Prefrontal Cortex": [ - [ - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" - ], - [ - "INIA_MacFas_Pf_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex control (Jan10) RMA **" - ], - [ - "INIA_MacFas_PfE_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex ethanol (Jan10) RMA **" - ], - [ - "VCUSal_1006_R", - "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" - ], - [ - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" - ], - [ - "VCUSal_1206_R", - "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" - ], - [ - "VCU_PF_Air_0111_R", - "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_Et_0111_R", - "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_AvE_0111_Ss", - "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" - ], - [ - "VCUEt_vs_Sal_0806_R", - "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" - ], - [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], - [ - "VCUSal_0806_R", - "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" - ] - ], - "Primary Visual Cortex": [ - [ - "KIN_YSM_V1C_0711", - "KIN/YSM Human V1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "HBTRC-MLVC_0611", - "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_N_0611", - "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_AD_0611", - "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_HD_0611", - "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" - ] - ] - }, - "HLC": { - "Genotypes": [ - [ - "HLCGeno", - "HLC Genotypes" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], - [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], - [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], - [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Phenotypes": [ - [ - "HLCPublish", - "HLC Published Phenotypes" - ] - ] - }, - "HSB": { - "Amygdala": [ - [ - "KIN_YSM_AMY_0711", - "KIN/YSM Human AMY Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "INIA_AmgCoh_0311", - "INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA" - ], - [ - "INIA_Amg_BLA_RMA_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA" - ], - [ - "INIA_Amg_BLA_RMA_M_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male" - ], - [ - "INIA_Amg_BLA_RMA_F_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female" - ], - [ - "INIA_MacFas_AMGc_RMA_0110", - "INIA Macaca fasicularis Amygdala control (Jan10) RMA **" - ], - [ - "INIA_MacFas_AMGe_RMA_0110", - "INIA Macaca fasicularis Amygdala ethanol (Jan10) RMA **" - ] - ], - "Caudal Ganglionic Eminence": [ - [ - "KIN_YSM_CGE_0711", - "KIN/YSM Human CGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Cerebellar Cortex": [ - [ - "KIN_YSM_CBC_0711", - "KIN/YSM Human CBC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Diencephalon": [ - [ - "KIN_YSM_DIE_0711", - "KIN/YSM Human DIE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Dorsal Thalamus": [ - [ - "KIN_YSM_DTH_0711", - "KIN/YSM Human DTH Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Dorsolateral Prefrontal Cortex": [ - [ - "KIN_YSM_DFC_0711", - "KIN/YSM Human DFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Frontal Cerebral Wall": [ - [ - "KIN_YSM_FC_0711", - "KIN/YSM Human FC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Genotypes": [ - [ - "HSBGeno", - "HSB Genotypes" - ] - ], - "Hippocampus": [ - [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], - [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], - [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" - ], - [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" - ], - [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" - ], - [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" - ], - [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" - ], - [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" - ], - [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" - ], - [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" - ], - [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" - ], - [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" - ], - [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" - ], - [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" - ], - [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" - ], - [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], - [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSE_0909", - "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" - ], - [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ] - ], - "Inferior Temporal Cortex": [ - [ - "KIN_YSM_ITC_0711", - "KIN/YSM Human ITC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Lateral Ganglionic Eminence": [ - [ - "KIN_YSM_LGE_0711", - "KIN/YSM Human LGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Medial Ganglionic Eminence": [ - [ - "KIN_YSM_MGE_0711", - "KIN/YSM Human MGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Medial Prefrontal Cortex": [ - [ - "KIN_YSM_MFC_0711", - "KIN/YSM Human MFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Mediodorsal Nucleus of Thalamus": [ - [ - "KIN_YSM_MD_0711", - "KIN/YSM Human MD Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Occipital Cerebral Wall": [ - [ - "KIN_YSM_OC_0711", - "KIN/YSM Human OC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Orbital Prefrontal Cortex": [ - [ - "KIN_YSM_OFC_0711", - "KIN/YSM Human OFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Parietal Cerebral Wall": [ - [ - "KIN_YSM_PC_0711", - "KIN/YSM Human PC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Phenotypes": [ - [ - "HSBPublish", - "HSB Published Phenotypes" - ] - ], - "Posterior Inferior Parietal Cortex": [ - [ - "KIN_YSM_IPC_0711", - "KIN/YSM Human IPC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Posterior Superior Temporal Cortex": [ - [ - "KIN_YSM_STC_0711", - "KIN/YSM Human STC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Auditory (A1) Cortex": [ - [ - "KIN_YSM_A1C_0711", - "KIN/YSM Human A1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Motor (M1) Cortex": [ - [ - "KIN_YSM_M1C_0711", - "KIN/YSM Human M1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Somatosensory (S1) Cortex": [ - [ - "KIN_YSM_S1C_0711", - "KIN/YSM Human S1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Visual Cortex": [ - [ - "KIN_YSM_V1C_0711", - "KIN/YSM Human V1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "HBTRC-MLVC_0611", - "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_N_0611", - "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_AD_0611", - "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_HD_0611", - "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" - ] - ], - "Striatum": [ - [ - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "KIN_YSM_STR_0711", - "KIN/YSM Human STR Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "OHSU_HS-CC_ILMStr_0211", - "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" - ], - [ - "UTHSC_Striatum_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" - ], - [ - "UTHSC_Str_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10) RankInv" - ], - [ - "UTHSC_1107_RankInv", - "HQF BXD Striatum ILM6.1 (Nov07) RankInv" - ], - [ - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], - [ - "SA_M2_0905_M", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" - ], - [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" - ], - [ - "SA_M2_0405_MC", - "HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean" - ], - [ - "SA_M2_0405_RC", - "HBP Rosen Striatum M430V2 (Apr05) RMA Clean" - ], - [ - "SA_M2_0405_PC", - "HBP Rosen Striatum M430V2 (Apr05) PDNN Clean" - ], - [ - "SA_M2_0405_SS", - "HBP Rosen Striatum M430V2 (Apr05) SScore" - ], - [ - "SA_M2_0405_RR", - "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" - ], - [ - "Striatum_Exon_0209", - "HQF Striatum Exon (Feb09) RMA" - ], - [ - "DevStriatum_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" - ] - ], - "Temporal Cerebral Wall": [ - [ - "KIN_YSM_TC_0711", - "KIN/YSM Human TC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Upper (Rostral) Rhombic Lip": [ - [ - "KIN_YSM_URL_0711", - "KIN/YSM Human URL Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Ventral Forebrain": [ - [ - "KIN_YSM_VF_0711", - "KIN/YSM Human VF Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Ventrolateral Prefrontal Cortex": [ - [ - "KIN_YSM_VFC_0711", - "KIN/YSM Human VFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ] - } - }, - "macaque monkey": { - "Macaca-fasicularis": { - "Amygdala": [ - [ - "KIN_YSM_AMY_0711", - "KIN/YSM Human AMY Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "INIA_AmgCoh_0311", - "INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA" - ], - [ - "INIA_Amg_BLA_RMA_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA" - ], - [ - "INIA_Amg_BLA_RMA_M_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male" - ], - [ - "INIA_Amg_BLA_RMA_F_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female" - ], - [ - "INIA_MacFas_AMGc_RMA_0110", - "INIA Macaca fasicularis Amygdala control (Jan10) RMA **" - ], - [ - "INIA_MacFas_AMGe_RMA_0110", - "INIA Macaca fasicularis Amygdala ethanol (Jan10) RMA **" - ] - ], - "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" - ], - [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], - [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ], - [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], - [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], - [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], - [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - ], - [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], - [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], - [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], - [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], - [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" - ], - [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" - ], - [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" - ] - ], - "Genotypes": [ - [ - "Macaca-fasicularisGeno", - "Macaca-fasicularis Genotypes" - ] - ], - "Hippocampus": [ - [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], - [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], - [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" - ], - [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" - ], - [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" - ], - [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" - ], - [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" - ], - [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" - ], - [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" - ], - [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" - ], - [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" - ], - [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" - ], - [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" - ], - [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" - ], - [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" - ], - [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], - [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" - 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] - ], - "Phenotypes": [ - [ - "Macaca-fasicularisPublish", - "Macaca-fasicularis Published Phenotypes" - ] - ], - "Prefrontal Cortex": [ - [ - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" - ], - [ - "INIA_MacFas_Pf_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex control (Jan10) RMA **" - ], - [ - "INIA_MacFas_PfE_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex ethanol (Jan10) RMA **" - ], - [ - "VCUSal_1006_R", - "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" - ], - [ - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" - ], - [ - "VCUSal_1206_R", - "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" - ], - [ - "VCU_PF_Air_0111_R", - "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_Et_0111_R", - "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_AvE_0111_Ss", - "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" - ], - [ - "VCUEt_vs_Sal_0806_R", - "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" - ], - [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], - [ - "VCUSal_0806_R", - "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" - ] - ] - } - }, - "mouse": { - "AKXD": { - "Genotypes": [ - [ - "AKXDGeno", - "AKXD Genotypes" - ] - ], - "Mammary Tumors": [ - [ - "NCI_Mam_Tum_RMA_0409", - "NCI Mammary M430v2 (Apr09) RMA" - ], - [ - "NCI_Agil_Mam_Tum_RMA_0409", - "NCI Mammary LMT miRNA v2 (Apr09) RMA" - ], - [ - "MA_M_0704_R", - "NCI Mammary mRNA M430 (July04) RMA" - ], - [ - "MA_M_0704_M", - "NCI Mammary mRNA M430 (July04) MAS5" - ] - ], - "Phenotypes": [ - [ - "AKXDPublish", - "AKXD Published Phenotypes" - ] - ] - }, - "AXBXA": { - "Eye": [ - [ - "Eye_AXBXA_1008_RankInv", - "Eye AXBXA Illumina V6.2(Oct08) RankInv Beta" - ], - [ - "Eye_M2_0908_R", - "Eye M430v2 (Sep08) RMA" - ], - [ - "Eye_M2_0908_R_NB", - "Eye M430v2 Mutant Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_ND", - "Eye M430v2 WT Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_WTWT", - "Eye M430v2 WT WT (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" - ], - [ - "BXD_GLA_0911", - "BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **" - ], - [ - "UIOWA_Eye_RMA_0906", - "UIOWA Eye mRNA RAE230v2 (Sep06) RMA" - ] - ], - "Genotypes": [ - [ - "AXBXAGeno", - "AXBXA Genotypes" - ] - ], - "Phenotypes": [ - [ - "AXBXAPublish", - "AXBXA Published Phenotypes" - ] - ] - }, - "B6BTBRF2": { - "Genotypes": [ - [ - "B6BTBRF2Geno", - "B6BTBRF2 Genotypes" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], - [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], - [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], - [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Phenotypes": [ - [ - "B6BTBRF2Publish", - "B6BTBRF2 Published Phenotypes" - ] - ] - }, - "B6D2F2": { - "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" - ], - [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], - [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ], - [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], - [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], - [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], - [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - 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"BDF2-1999 Genotypes" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], - [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], - [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], - [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Phenotypes": [ - [ - "BDF2-1999Publish", - "BDF2-1999 Published Phenotypes" - ] - ] - }, - "BDF2-2005": { - "Genotypes": [ - [ - "BDF2-2005Geno", - "BDF2-2005 Genotypes" - ] - ], - "Phenotypes": [ - [ - "BDF2-2005Publish", - "BDF2-2005 Published Phenotypes" - ] - ], - "Striatum": [ - [ - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "KIN_YSM_STR_0711", - "KIN/YSM Human STR Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "OHSU_HS-CC_ILMStr_0211", - "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" - ], - [ - "UTHSC_Striatum_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" - ], - [ - "UTHSC_Str_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10) RankInv" - ], - [ - "UTHSC_1107_RankInv", - "HQF BXD Striatum ILM6.1 (Nov07) RankInv" - ], - [ - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], - [ - "SA_M2_0905_M", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" - ], - [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" - ], - [ - "SA_M2_0405_MC", - "HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean" - ], - [ - "SA_M2_0405_RC", - "HBP Rosen Striatum M430V2 (Apr05) RMA Clean" - ], - [ - "SA_M2_0405_PC", - "HBP Rosen Striatum M430V2 (Apr05) PDNN Clean" - ], - [ - "SA_M2_0405_SS", - "HBP Rosen Striatum M430V2 (Apr05) SScore" - ], - [ - "SA_M2_0405_RR", - "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" - ], - [ - "Striatum_Exon_0209", - "HQF Striatum Exon (Feb09) RMA" - ], - [ - "DevStriatum_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" - ] - ] - }, - "BHF2": { - "Adipose": [ - [ - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_MALE", - "UCLA CTB6B6CTF2 Adipose Male mlratio **" - ], - [ - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE", - "UCLA CTB6B6CTF2 Adipose Female mlratio **" - ], - [ - "UCLA_BHHBF2_ADIPOSE_MALE", - "UCLA BHHBF2 Adipose Male Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_FEMALE", - "UCLA BHHBF2 Adipose Female Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_2005", - "UCLA BHHBF2 Adipose (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_2005", - "UCLA CTB6/B6CTF2 Adipose (2005) mlratio **" - ], - [ - "UCLA_BHF2_ADIPOSE_0605", - "UCLA BHF2 Adipose (June05) mlratio" - ] - ], - "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" - ], - [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], - [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ], - [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], - [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], - [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], - [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - ], - [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], - [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], - [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], - [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], - [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" - ], - [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" - ], - [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" - ] - ], - "Genotypes": [ - [ - "BHF2Geno", - "BHF2 Genotypes" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], - [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], - [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], - [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Muscle": [ - [ - "EPFLMouseMuscleRMA1211", - "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleCDRMA1211", - "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleHFDRMA1211", - "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", - "UCLA CTB6B6CTF2 Muscle Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_MALE", - "UCLA CTB6B6CTF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_FEMALE", - "UCLA BHHBF2 Muscle Female Only" - ], - [ - "UCLA_BHHBF2_MUSCLE_MALE", - "UCLA BHHBF2 Muscle Male Only" - ], - [ - "UCLA_BHF2_MUSCLE_MALE", - "UCLA BHF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_2005", - "UCLA BHHBF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_2005", - "UCLA CTB6/B6CTF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_0605", - "UCLA BHF2 Muscle (June05) mlratio **" - ] - ], - "Phenotypes": [ - [ - "BHF2Publish", - "BHF2 Published Phenotypes" - ] - ] - }, - "BHHBF2": { - "Adipose": [ - [ - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_MALE", - "UCLA CTB6B6CTF2 Adipose Male mlratio **" - ], - [ - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE", - "UCLA CTB6B6CTF2 Adipose Female mlratio **" - ], - [ - "UCLA_BHHBF2_ADIPOSE_MALE", - "UCLA BHHBF2 Adipose Male Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_FEMALE", - "UCLA BHHBF2 Adipose Female Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_2005", - "UCLA BHHBF2 Adipose (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_2005", - "UCLA CTB6/B6CTF2 Adipose (2005) mlratio **" - ], - [ - "UCLA_BHF2_ADIPOSE_0605", - "UCLA BHF2 Adipose (June05) mlratio" - ] - ], - "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" - ], - [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], - [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ], - [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], - [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], - [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], - [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - ], - [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], - [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], - [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], - [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], - [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" - ], - [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" - ], - [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" - ] - ], - "Genotypes": [ - [ - "BHHBF2Geno", - "BHHBF2 Genotypes" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], - [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], - [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], - [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Muscle": [ - [ - "EPFLMouseMuscleRMA1211", - "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleCDRMA1211", - "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleHFDRMA1211", - "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", - "UCLA CTB6B6CTF2 Muscle Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_MALE", - "UCLA CTB6B6CTF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_FEMALE", - "UCLA BHHBF2 Muscle Female Only" - ], - [ - "UCLA_BHHBF2_MUSCLE_MALE", - "UCLA BHHBF2 Muscle Male Only" - ], - [ - "UCLA_BHF2_MUSCLE_MALE", - "UCLA BHF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_2005", - "UCLA BHHBF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_2005", - "UCLA CTB6/B6CTF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_0605", - "UCLA BHF2 Muscle (June05) mlratio **" - ] - ], - "Phenotypes": [ - [ - "BHHBF2Publish", - "BHHBF2 Published Phenotypes" - ] - ] - }, - "BXD": { - "Amygdala": [ - [ - "KIN_YSM_AMY_0711", - "KIN/YSM Human AMY Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "INIA_AmgCoh_0311", - "INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA" - ], - [ - "INIA_Amg_BLA_RMA_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA" - ], - [ - "INIA_Amg_BLA_RMA_M_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male" - ], - [ - "INIA_Amg_BLA_RMA_F_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female" - ], - [ - "INIA_MacFas_AMGc_RMA_0110", - "INIA Macaca fasicularis Amygdala control (Jan10) RMA **" - ], - [ - "INIA_MacFas_AMGe_RMA_0110", - "INIA Macaca fasicularis Amygdala ethanol (Jan10) RMA **" - ] - ], - "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" - ], - [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], - [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ], - [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], - [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], - [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], - [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - ], - [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], - [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], - [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], - [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], - [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" - ], - [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" - ], - [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" - ] - ], - "Cartilage": [ - [ - "UCLA_BXDBXH_CARTILAGE_V2", - "UCLA BXD and BXH Cartilage v2" - ], - [ - "UCLA_BXHBXD_CARTILAGE_V2", - "UCLA BXH and BXD Cartilage v2" - ], - [ - "UCLA_BXDBXH_CARTILAGE", - "UCLA BXD and BXH Cartilage" - ], - [ - "UCLA_BXHBXD_CARTILAGE", - "UCLA BXH and BXD Cartilage" - ], - [ - "UCLA_BXD_CARTILAGE", - "UCLA BXD Cartilage" - ], - [ - "UCLA_BXH_CARTILAGE", - "UCLA BXH Cartilage" - ] - ], - "Cerebellum": [ - [ - "HBTRC-MLC_0611", - "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLC_N_0611", - "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLC_AD_0611", - "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLC_HD_0611", - "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" - ], - [ - "GCB_M2_0505_M", - "GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5" - ], - [ - "GCB_M2_0505_R", - "GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA" - ], - [ - "GCB_M2_0505_P", - "GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN" - ], - [ - "CB_M_0305_R", - "SJUT Cerebellum mRNA M430 (Mar05) RMA" - ], - [ - "CB_M_0305_M", - "SJUT Cerebellum mRNA M430 (Mar05) MAS5" - ], - [ - "CB_M_0305_P", - "SJUT Cerebellum mRNA M430 (Mar05) PDNN" - ], - [ - "CB_M_1004_R", - "SJUT Cerebellum mRNA M430 (Oct04) RMA" - ], - [ - "CB_M_1004_M", - "SJUT Cerebellum mRNA M430 (Oct04) MAS5" - ], - [ - "CB_M_1004_P", - "SJUT Cerebellum mRNA M430 (Oct04) PDNN" - ], - [ - "CB_M_1003_M", - "SJUT Cerebellum mRNA M430 (Oct03) MAS5" - ] - ], - "Eye": [ - [ - "Eye_AXBXA_1008_RankInv", - "Eye AXBXA Illumina V6.2(Oct08) RankInv Beta" - ], - [ - "Eye_M2_0908_R", - "Eye M430v2 (Sep08) RMA" - ], - [ - "Eye_M2_0908_R_NB", - "Eye M430v2 Mutant Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_ND", - "Eye M430v2 WT Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_WTWT", - "Eye M430v2 WT WT (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" - ], - [ - "BXD_GLA_0911", - "BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **" - ], - [ - "UIOWA_Eye_RMA_0906", - "UIOWA Eye mRNA RAE230v2 (Sep06) RMA" - ] - ], - "Genotypes": [ - [ - "BXDGeno", - "BXD Genotypes" - ] - ], - "Hematopoietic Cells": [ - [ - "UMCG_0907_HemaStem_ori", - "UMCG Stem Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_HemaStem", - "UMCG Stem Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "UMCG_0907_Pro_ori", - "UMCG Progenitor Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_Pro", - "UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "UMCG_0907_Eryth_ori", - "UMCG Erythroid Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_Eryth", - "UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "UMCG_0907_Myeloid_ori", - "UMCG Myeloid Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_Myeloid", - "UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "HC_U_0304_R", - "GNF Stem Cells U74Av2 (Mar04) RMA" - ] - ], - "Hippocampus": [ - [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], - [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], - [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" - ], - [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" - ], - [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" - ], - [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" - ], - [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" - ], - [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" - ], - [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" - ], - [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" - ], - [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" - ], - [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" - ], - [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" - ], - [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" - ], - [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" - ], - [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], - [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSE_0909", - "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" - ], - [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ] - ], - "Hypothalamus": [ - [ - "INIA_Hyp_RMA_1110", - "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)" - ], - [ - "INIA_Hyp_M_RMA_1110", - "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Male" - ], - [ - "INIA_Hyp_F_RMA_1110", - "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female" - ] - ], - "Kidney": [ - [ - "MA_M2F_0706_R", - "Mouse kidney M430v2 Female (Aug06) RMA" - ], - [ - "MA_M2M_0706_R", - "Mouse kidney M430v2 Male (Aug06) RMA" - ], - [ - "MA_M2_0806_R", - "Mouse kidney M430v2 Sex Balanced (Aug06) RMA" - ], - [ - "MA_M2_0806_P", - "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" - ], - [ - "MA_M2_0706_P", - "Mouse Kidney M430v2 (Jul06) PDNN" - ], - [ - "MA_M2_0706_R", - "Mouse Kidney M430v2 (Jul06) RMA" - ], - [ - "KI_2A_0405_M", - "MDC/CAS/ICL Kidney 230A (Apr05) MAS5" - ], - [ - "KI_2A_0405_Rz", - "MDC/CAS/ICL Kidney 230A (Apr05) RMA 2z+8" - ], - [ - "KI_2A_0405_R", - "MDC/CAS/ICL Kidney 230A (Apr05) RMA" - ] - ], - "Leucocytes": [ - [ - "Illum_BXD_PBL_1108", - "UWA Illumina PBL (Nov08) RSN **" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], - [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], - [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], - [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Lung": [ - [ - "OXUKHS_ILMLung_RI0510", - "OX UK HS ILM6v1.1 Lung (May 2010) RankInv" - ], - [ - "HZI_0408_R", - "HZI Lung M430v2 (Apr08) RMA" - ], - [ - "HZI_0408_M", - "HZI Lung M430v2 (Apr08) MAS5" - ] - ], - "Midbrain": [ - [ - "VUBXDMouseMidBrainQ0212", - "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (Feb12) Quantile" - ] - ], - "Muscle": [ - [ - "EPFLMouseMuscleRMA1211", - "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleCDRMA1211", - "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleHFDRMA1211", - "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", - "UCLA CTB6B6CTF2 Muscle Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_MALE", - "UCLA CTB6B6CTF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_FEMALE", - "UCLA BHHBF2 Muscle Female Only" - ], - [ - "UCLA_BHHBF2_MUSCLE_MALE", - "UCLA BHHBF2 Muscle Male Only" - ], - [ - "UCLA_BHF2_MUSCLE_MALE", - "UCLA BHF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_2005", - "UCLA BHHBF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_2005", - "UCLA CTB6/B6CTF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_0605", - "UCLA BHF2 Muscle (June05) mlratio **" - ] - ], - "Neocortex": [ - [ - "DevNeocortex_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "DevNeocortex_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "HQFNeoc_1210v2_RankInv", - "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" - ], - [ - "HQFNeoc_1210_RankInv", - "HQF BXD Neocortex ILM6v1.1 (Dec10) RankInv" - ], - [ - "HQFNeoc_0208_RankInv", - "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" - ], - [ - "DevNeocortex_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv **" - ], - [ - "DevNeocortex_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv **" - ] - ], - "Nucleus Accumbens": [ - [ - "INIA_MacFas_Ac_RMA_0110", - "INIA Macaca fasicularis Nucleus Accumbens control (Jan10) RMA **" - ], - [ - "INIA_MacFas_Ae_RMA_0110", - "INIA Macaca fasicularis Nucleus Accumbens ethanol (Jan10) RMA **" - ], - [ - "VCUSalo_1007_R", - "VCU BXD NA Sal M430 2.0 (Oct07) RMA" - ], - [ - "VCUEtOH_1007_R", - "VCU BXD NA EtOH M430 2.0 (Oct07) RMA **" - ], - [ - "VCUSal_1007_R", - "VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore **" - ] - ], - "Phenotypes": [ - [ - "BXDPublish", - "BXD Published Phenotypes" - ] - ], - "Prefrontal Cortex": [ - [ - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" - ], - [ - "INIA_MacFas_Pf_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex control (Jan10) RMA **" - ], - [ - "INIA_MacFas_PfE_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex ethanol (Jan10) RMA **" - ], - [ - "VCUSal_1006_R", - "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" - ], - [ - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" - ], - [ - "VCUSal_1206_R", - "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" - ], - [ - "VCU_PF_Air_0111_R", - "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_Et_0111_R", - "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_AvE_0111_Ss", - "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" - ], - [ - "VCUEt_vs_Sal_0806_R", - "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" - ], - [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], - [ - "VCUSal_0806_R", - "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" - ] - ], - "Retina": [ - [ - "Illum_Retina_BXD_RankInv0410", - "HEI Retina Illumina V6.2 (April 2010) RankInv" - ], - [ - "B6D2ONCILM_0412", - "B6D2 ONC Illumina v6.1 (Apr12) RankInv **" - ], - [ - "ONCRetILM6_0412", - "ONC Retina Illumina V6.2 (Apr12) RankInv **" - ], - [ - "G2HEIONCRetILM6_0911", - "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" - ], - [ - "HEIONCRetILM6_0911", - "HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" - ], - [ - "HEIONCvsCRetILM6_0911", - "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" - ], - [ - "ILM_Retina_BXD_F_RankInv1210", - "HEI Retina Females Illumina V6.2 (Dec10) RankInv **" - ], - [ - "ILM_Retina_BXD_M_RankInv1210", - "HEI Retina Males Illumina V6.2 (Dec10) RankInv **" - ], - [ - "ILM_Retina_BXD_FM_RankInv1210", - "HEI Retina F-M Illumina V6.2 (Dec10) RankInv **" - ], - [ - "G2NEI_ILM_Retina_BXD_RI0410", - "G2NEI Retina Illumina V6.2 (April 2010) RankInv **" - ] - ], - "Spleen": [ - [ - "UTHSC_SPL_RMA_1210", - "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" - ], - [ - "UTHSC_SPL_RMA_1010", - "UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA" - ], - [ - "IoP_SPL_RMA_0509", - "IoP Affy MOE 430v2 Spleen (May09) RMA" - ], - [ - "Illum_BXD_Spl_1108", - "UWA Illumina Spleen (Nov08) RSN **" - ], - [ - "UTK_BXDSpl_VST_0110", - "UTK Spleen ILM6.1 (Jan10) VST" - ], - [ - "STSPL_1107_R", - "Stuart Spleen M430v2 (Nov07) RMA" - ] - ], - "Striatum": [ - [ - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "KIN_YSM_STR_0711", - "KIN/YSM Human STR Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "OHSU_HS-CC_ILMStr_0211", - "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" - ], - [ - "UTHSC_Striatum_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" - ], - [ - "UTHSC_Str_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10) RankInv" - ], - [ - "UTHSC_1107_RankInv", - "HQF BXD Striatum ILM6.1 (Nov07) RankInv" - ], - [ - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ], - [ - "SA_M2_0905_M", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" - ], - [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" - ], - [ - "SA_M2_0405_MC", - "HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean" - ], - [ - "SA_M2_0405_RC", - "HBP Rosen Striatum M430V2 (Apr05) RMA Clean" - ], - [ - "SA_M2_0405_PC", - "HBP Rosen Striatum M430V2 (Apr05) PDNN Clean" - ], - [ - "SA_M2_0405_SS", - "HBP Rosen Striatum M430V2 (Apr05) SScore" - ], - [ - "SA_M2_0405_RR", - "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" - ], - [ - "Striatum_Exon_0209", - "HQF Striatum Exon (Feb09) RMA" - ], - [ - "DevStriatum_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" - ] - ], - "T Cell (helper)": [ - [ - "RTHC_0211_R", - "HZI Thelp M430v2 (Feb11) RMA" - ] - ], - "T Cell (regulatory)": [ - [ - "RTC_1106_R", - "HZI Treg M430v2 (Feb11) RMA" - ] - ], - "Thymus": [ - [ - "Illum_BXD_Thy_1108", - "UWA Illumina Thymus (Nov08) RSN **" - ] - ], - "Ventral Tegmental Area": [ - [ - "VCUEtvsSal_0609_R", - "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **" - ], - [ - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" - ], - [ - "VCUSal_0609_R", - "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" - ] - ] - }, - "BXH": { - "Cartilage": [ - [ - "UCLA_BXDBXH_CARTILAGE_V2", - "UCLA BXD and BXH Cartilage v2" - ], - [ - "UCLA_BXHBXD_CARTILAGE_V2", - "UCLA BXH and BXD Cartilage v2" - ], - [ - "UCLA_BXDBXH_CARTILAGE", - "UCLA BXD and BXH Cartilage" - ], - [ - "UCLA_BXHBXD_CARTILAGE", - "UCLA BXH and BXD Cartilage" - ], - [ - "UCLA_BXD_CARTILAGE", - "UCLA BXD Cartilage" - ], - [ - "UCLA_BXH_CARTILAGE", - "UCLA BXH Cartilage" - ] - ], - "Genotypes": [ - [ - "BXHGeno", - "BXH Genotypes" - ] - ], - "Phenotypes": [ - [ - "BXHPublish", - "BXH Published Phenotypes" - ] - ] - }, - "CTB6F2": { - "Adipose": [ - [ - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_MALE", - "UCLA CTB6B6CTF2 Adipose Male mlratio **" - ], - [ - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE", - "UCLA CTB6B6CTF2 Adipose Female mlratio **" - ], - [ - "UCLA_BHHBF2_ADIPOSE_MALE", - "UCLA BHHBF2 Adipose Male Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_FEMALE", - "UCLA BHHBF2 Adipose Female Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_2005", - "UCLA BHHBF2 Adipose (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_ADIPOSE_2005", - "UCLA CTB6/B6CTF2 Adipose (2005) mlratio **" - ], - [ - "UCLA_BHF2_ADIPOSE_0605", - "UCLA BHF2 Adipose (June05) mlratio" - ] - ], - "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ], - [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" - ], - [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], - [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ], - [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ], - [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], - [ - "IBR_M_0606_R", - "INIA Brain mRNA M430 (Jun06) RMA" - ], - [ - "IBR_M_0106_P", - "INIA Brain mRNA M430 (Jan06) PDNN" - ], - [ - "IBR_M_0106_R", - "INIA Brain mRNA M430 (Jan06) RMA" - ], - [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], - [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], - [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], - [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], - [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" - ], - [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" - ], - [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" - ] - ], - "Genotypes": [ - [ - "CTB6F2Geno", - "CTB6F2 Genotypes" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], - [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], - [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], - [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Muscle": [ - [ - "EPFLMouseMuscleRMA1211", - "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleCDRMA1211", - "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleHFDRMA1211", - "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", - "UCLA CTB6B6CTF2 Muscle Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_MALE", - "UCLA CTB6B6CTF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_FEMALE", - "UCLA BHHBF2 Muscle Female Only" - ], - [ - "UCLA_BHHBF2_MUSCLE_MALE", - "UCLA BHHBF2 Muscle Male Only" - ], - [ - "UCLA_BHF2_MUSCLE_MALE", - "UCLA BHF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], - [ - "UCLA_BHHBF2_MUSCLE_2005", - "UCLA BHHBF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_2005", - "UCLA CTB6/B6CTF2 Muscle (2005) mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_0605", - "UCLA BHF2 Muscle (June05) mlratio **" - ] - ], - "Phenotypes": [ - [ - "CTB6F2Publish", - "CTB6F2 Published Phenotypes" + "KIN_YSM_VFC_0711", + "KIN/YSM Human VFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" ] ] - }, - "CXB": { - "Genotypes": [ - [ - "CXBGeno", - "CXB Genotypes" - ] - ], - "Hippocampus": [ - [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], - [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], - [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" - ], - [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" - ], - [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" - ], - [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" - ], - [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" - ], - [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" - ], - [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" - ], - [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" - ], - [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" - ], - [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" - ], - [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" - ], - [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" - ], - [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" - ], - [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], - [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSE_0909", - "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" - ], - [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], + } + }, + "macaque monkey": { + "Macaca-fasicularis": { + "Amygdala": [ [ - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" + "INIA_MacFas_AMGc_RMA_0110", + "INIA Macaca fasicularis Amygdala control (Jan10) RMA **" ], [ - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], + "INIA_MacFas_AMGe_RMA_0110", + "INIA Macaca fasicularis Amygdala ethanol (Jan10) RMA **" + ] + ], + "Brain": [ [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" + "INIA_MacFas_brain_RMA_0110", + "INIA Macaca fasicularis Brain (Jan10) RMA **" ] ], - "Phenotypes": [ + "Genotypes": [ [ - "CXBPublish", - "CXB Published Phenotypes" + "Macaca-fasicularisGeno", + "Macaca-fasicularis Genotypes" ] ], - "Spleen": [ + "Hippocampus": [ [ - "UTHSC_SPL_RMA_1210", - "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" + "INIA_MacFas_Hc_RMA_0110", + "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" ], [ - "UTHSC_SPL_RMA_1010", - "UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA" - ], + "INIA_MacFas_He_RMA_0110", + "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" + ] + ], + "Nucleus Accumbens": [ [ - "IoP_SPL_RMA_0509", - "IoP Affy MOE 430v2 Spleen (May09) RMA" + "INIA_MacFas_Ac_RMA_0110", + "INIA Macaca fasicularis Nucleus Accumbens control (Jan10) RMA **" ], [ - "Illum_BXD_Spl_1108", - "UWA Illumina Spleen (Nov08) RSN **" - ], + "INIA_MacFas_Ae_RMA_0110", + "INIA Macaca fasicularis Nucleus Accumbens ethanol (Jan10) RMA **" + ] + ], + "Phenotypes": [ [ - "UTK_BXDSpl_VST_0110", - "UTK Spleen ILM6.1 (Jan10) VST" + "Macaca-fasicularisPublish", + "Macaca-fasicularis Published Phenotypes" + ] + ], + "Prefrontal Cortex": [ + [ + "INIA_MacFas_Pf_RMA_0110", + "INIA Macaca fasicularis Prefrontal Cortex control (Jan10) RMA **" ], [ - "STSPL_1107_R", - "Stuart Spleen M430v2 (Nov07) RMA" + "INIA_MacFas_PfE_RMA_0110", + "INIA Macaca fasicularis Prefrontal Cortex ethanol (Jan10) RMA **" ] ] - }, - "HS": { + } + }, + "mouse": { + "AKXD": { "Genotypes": [ [ - "HSGeno", - "HS Genotypes" + "AKXDGeno", + "AKXD Genotypes" ] ], - "Hippocampus": [ - [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], - [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], - [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" - ], - [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" - ], - [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" - ], - [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" - ], + "Mammary Tumors": [ [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" + "NCI_Agil_Mam_Tum_RMA_0409", + "NCI Mammary LMT miRNA v2 (Apr09) RMA" ], [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" + "MA_M_0704_R", + "NCI Mammary mRNA M430 (July04) RMA" ], [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" - ], + "MA_M_0704_M", + "NCI Mammary mRNA M430 (July04) MAS5" + ] + ], + "Phenotypes": [ [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" - ], + "AKXDPublish", + "AKXD Published Phenotypes" + ] + ] + }, + "AXBXA": { + "Eye": [ [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" - ], + "Eye_AXBXA_1008_RankInv", + "Eye AXBXA Illumina V6.2(Oct08) RankInv Beta" + ] + ], + "Genotypes": [ [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" - ], + "AXBXAGeno", + "AXBXA Genotypes" + ] + ], + "Phenotypes": [ [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" - ], + "AXBXAPublish", + "AXBXA Published Phenotypes" + ] + ] + }, + "B6BTBRF2": { + "Genotypes": [ [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" - ], + "B6BTBRF2Geno", + "B6BTBRF2 Genotypes" + ] + ], + "Liver": [ [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" + "LVF2_M_0704_R", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" ], [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], + "LVF2_M_0704_M", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" + ] + ], + "Phenotypes": [ [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], + "B6BTBRF2Publish", + "B6BTBRF2 Published Phenotypes" + ] + ] + }, + "B6D2F2": { + "Brain": [ [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" ], [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" + "BRF2_M_0805_M", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" ], [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" + "BRF2_M_0805_P", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" ], [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" + "BRF2_M_0304_P", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" ], [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" + "BRF2_M_0304_R", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" ], [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" - ], + "BRF2_M_0304_M", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" + ] + ], + "Genotypes": [ [ - "UT_ILM_BXD_hipp_RSE_0909", - "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" - ], + "B6D2F2Geno", + "B6D2F2 Genotypes" + ] + ], + "Phenotypes": [ [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], + "B6D2F2Publish", + "B6D2F2 Published Phenotypes" + ] + ] + }, + "BDF2-1999": { + "Genotypes": [ [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], + "BDF2-1999Geno", + "BDF2-1999 Genotypes" + ] + ], + "Liver": [ [ - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" - ], + "UCLA_BDF2_LIVER_1999", + "UCLA BDF2 Liver (1999) mlratio" + ] + ], + "Phenotypes": [ [ - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], + "BDF2-1999Publish", + "BDF2-1999 Published Phenotypes" + ] + ] + }, + "BDF2-2005": { + "Genotypes": [ [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" + "BDF2-2005Geno", + "BDF2-2005 Genotypes" ] ], - "Liver": [ + "Phenotypes": [ [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], + "BDF2-2005Publish", + "BDF2-2005 Published Phenotypes" + ] + ], + "Striatum": [ [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" ], [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" + "SA_M2_0905_M", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" ], [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], + "SA_M2_0905_P", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" + ] + ] + }, + "BHF2": { + "Adipose": [ [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" + "UCLA_BHF2_ADIPOSE_MALE", + "UCLA BHF2 Adipose Male mlratio" ], [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" + "UCLA_BHF2_ADIPOSE_FEMALE", + "UCLA BHF2 Adipose Female mlratio" ], [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], + "UCLA_BHF2_ADIPOSE_0605", + "UCLA BHF2 Adipose (June05) mlratio" + ] + ], + "Brain": [ [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" + "UCLA_BHF2_BRAIN_MALE", + "UCLA BHF2 Brain Male mlratio" ], [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" + "UCLA_BHF2_BRAIN_FEMALE", + "UCLA BHF2 Brain Female mlratio" ], [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], + "UCLA_BHF2_BRAIN_0605", + "UCLA BHF2 Brain (June05) mlratio" + ] + ], + "Genotypes": [ [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], + "BHF2Geno", + "BHF2 Genotypes" + ] + ], + "Liver": [ [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male mlratio" ], [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" + "UCLA_BHF2_LIVER_FEMALE", + "UCLA BHF2 Liver Female mlratio" ], [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], + "UCLA_BHF2_LIVER_0605", + "UCLA BHF2 Liver (June05) mlratio" + ] + ], + "Muscle": [ [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + "UCLA_BHF2_MUSCLE_MALE", + "UCLA BHF2 Muscle Male mlratio **" ], [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" + "UCLA_BHF2_MUSCLE_FEMALE", + "UCLA BHF2 Muscle Female mlratio **" ], [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], + "UCLA_BHF2_MUSCLE_0605", + "UCLA BHF2 Muscle (June05) mlratio **" + ] + ], + "Phenotypes": [ [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], + "BHF2Publish", + "BHF2 Published Phenotypes" + ] + ] + }, + "BHHBF2": { + "Adipose": [ [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" + "UCLA_BHHBF2_ADIPOSE_MALE", + "UCLA BHHBF2 Adipose Male Only" ], [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" + "UCLA_BHHBF2_ADIPOSE_FEMALE", + "UCLA BHHBF2 Adipose Female Only" ], [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" + "UCLA_BHHBF2_ADIPOSE_2005", + "UCLA BHHBF2 Adipose (2005) mlratio **" + ] + ], + "Brain": [ + [ + "UCLA_BHHBF2_BRAIN_MALE", + "UCLA BHHBF2 Brain Male Only" ], [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" + "UCLA_BHHBF2_BRAIN_FEMALE", + "UCLA BHHBF2 Brain Female Only" ], + [ + "UCLA_BHHBF2_BRAIN_2005", + "UCLA BHHBF2 Brain (2005) mlratio **" + ] + ], + "Genotypes": [ + [ + "BHHBF2Geno", + "BHHBF2 Genotypes" + ] + ], + "Liver": [ [ "UCLA_BHHBF2_LIVER_MALE", "UCLA BHHBF2 Liver Male Only" ], [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" + "UCLA_BHHBF2_LIVER_FEMALE", + "UCLA BHHBF2 Liver Female Only" ], [ "UCLA_BHHBF2_LIVER_2005", "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" ] ], - "Lung": [ + "Muscle": [ [ - "OXUKHS_ILMLung_RI0510", - "OX UK HS ILM6v1.1 Lung (May 2010) RankInv" + "UCLA_BHHBF2_MUSCLE_MALE", + "UCLA BHHBF2 Muscle Male Only" ], [ - "HZI_0408_R", - "HZI Lung M430v2 (Apr08) RMA" + "UCLA_BHHBF2_MUSCLE_FEMALE", + "UCLA BHHBF2 Muscle Female Only" ], [ - "HZI_0408_M", - "HZI Lung M430v2 (Apr08) MAS5" + "UCLA_BHHBF2_MUSCLE_2005", + "UCLA BHHBF2 Muscle (2005) mlratio **" ] ], "Phenotypes": [ [ - "HSPublish", - "HS Published Phenotypes" + "BHHBF2Publish", + "BHHBF2 Published Phenotypes" ] ] }, - "HS-CC": { - "Genotypes": [ - [ - "HS-CCGeno", - "HS-CC Genotypes" - ] - ], - "Phenotypes": [ - [ - "HS-CCPublish", - "HS-CC Published Phenotypes" - ] - ], - "Striatum": [ - [ - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "KIN_YSM_STR_0711", - "KIN/YSM Human STR Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], + "BXD": { + "Amygdala": [ [ - "OHSU_HS-CC_ILMStr_0211", - "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" + "INIA_AmgCoh_0311", + "INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA" ], [ - "UTHSC_Striatum_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" + "INIA_Amg_BLA_RMA_1110", + "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA" ], [ - "UTHSC_Str_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10) RankInv" + "INIA_Amg_BLA_RMA_M_1110", + "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male" ], [ - "UTHSC_1107_RankInv", - "HQF BXD Striatum ILM6.1 (Nov07) RankInv" - ], + "INIA_Amg_BLA_RMA_F_1110", + "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female" + ] + ], + "Brain": [ [ - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" + "BR_M2_1106_R", + "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" ], [ - "SA_M2_0905_M", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" + "BR_U_1105_P", + "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" ], [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" + "BR_U_0805_M", + "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" ], [ - "SA_M2_0405_MC", - "HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean" + "BR_U_0805_R", + "UTHSC Brain mRNA U74Av2 (Aug05) RMA" ], [ - "SA_M2_0405_RC", - "HBP Rosen Striatum M430V2 (Apr05) RMA Clean" + "BR_U_0805_P", + "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" ], [ - "SA_M2_0405_PC", - "HBP Rosen Striatum M430V2 (Apr05) PDNN Clean" - ], + "CB_M_0204_P", + "INIA Brain mRNA M430 (Feb04) PDNN" + ] + ], + "Cartilage": [ [ - "SA_M2_0405_SS", - "HBP Rosen Striatum M430V2 (Apr05) SScore" + "UCLA_BXDBXH_CARTILAGE_V2", + "UCLA BXD and BXH Cartilage v2" ], [ - "SA_M2_0405_RR", - "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" + "UCLA_BXDBXH_CARTILAGE", + "UCLA BXD and BXH Cartilage" ], [ - "Striatum_Exon_0209", - "HQF Striatum Exon (Feb09) RMA" + "UCLA_BXD_CARTILAGE", + "UCLA BXD Cartilage" + ] + ], + "Cerebellum": [ + [ + "CB_M_1004_M", + "SJUT Cerebellum mRNA M430 (Oct04) MAS5" ], [ - "DevStriatum_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" + "CB_M_1004_R", + "SJUT Cerebellum mRNA M430 (Oct04) RMA" ], [ - "DevStriatum_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" - ] - ] - }, - "LXS": { - "Genotypes": [ + "CB_M_1004_P", + "SJUT Cerebellum mRNA M430 (Oct04) PDNN" + ], [ - "LXSGeno", - "LXS Genotypes" + "CB_M_1003_M", + "SJUT Cerebellum mRNA M430 (Oct03) MAS5" ] ], - "Hippocampus": [ + "Eye": [ [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + "Eye_M2_0908_R", + "Eye M430v2 (Sep08) RMA" ], [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + "Eye_M2_0908_R_NB", + "Eye M430v2 Mutant Gpnmb (Sep08) RMA **" ], [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" + "Eye_M2_0908_R_ND", + "Eye M430v2 WT Gpnmb (Sep08) RMA **" ], [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" + "Eye_M2_0908_R_WT", + "Eye M430v2 WT Tyrp1 (Sep08) RMA **" ], [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" + "Eye_M2_0908_WTWT", + "Eye M430v2 WT WT (Sep08) RMA **" ], [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" + "Eye_M2_0908_R_MT", + "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" ], [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" + "BXD_GLA_0911", + "BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **" + ] + ], + "Genotypes": [ + [ + "BXDGeno", + "BXD Genotypes" + ] + ], + "Hematopoietic Cells": [ + [ + "UMCG_0907_HemaStem_ori", + "UMCG Stem Cells ILM6v1.1 (Apr09) original" ], [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" + "UMCG_0907_HemaStem", + "UMCG Stem Cells ILM6v1.1 (Apr09) transformed" ], [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" + "UMCG_0907_Pro_ori", + "UMCG Progenitor Cells ILM6v1.1 (Apr09) original" ], [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" + "UMCG_0907_Pro", + "UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed" ], [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" + "UMCG_0907_Eryth_ori", + "UMCG Erythroid Cells ILM6v1.1 (Apr09) original" ], [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" + "UMCG_0907_Eryth", + "UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed" ], [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" + "UMCG_0907_Myeloid_ori", + "UMCG Myeloid Cells ILM6v1.1 (Apr09) original" ], [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" + "UMCG_0907_Myeloid", + "UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed" ], + [ + "HC_U_0304_R", + "GNF Stem Cells U74Av2 (Mar04) RMA" + ] + ], + "Hippocampus": [ [ "HC_M2_0606_P", "Hippocampus Consortium M430v2 (Jun06) PDNN" @@ -4939,14 +1081,6 @@ "HC_M2_0606_R", "Hippocampus Consortium M430v2 (Jun06) RMA" ], - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], [ "UMUTAffyExon_0209_RMA", "UMUTAffy Hippocampus Exon (Feb09) RMA" @@ -4970,63 +1104,169 @@ [ "UT_ILM_BXD_hipp_RSE_0909", "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" + ] + ], + "Hypothalamus": [ + [ + "INIA_Hyp_RMA_1110", + "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)" ], [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" + "INIA_Hyp_M_RMA_1110", + "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Male" ], [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" + "INIA_Hyp_F_RMA_1110", + "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female" + ] + ], + "Kidney": [ + [ + "MA_M2F_0706_R", + "Mouse kidney M430v2 Female (Aug06) RMA" ], [ - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" + "MA_M2M_0706_R", + "Mouse kidney M430v2 Male (Aug06) RMA" ], [ - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" + "MA_M2_0806_R", + "Mouse kidney M430v2 Sex Balanced (Aug06) RMA" ], [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" + "MA_M2_0806_P", + "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" + ], + [ + "MA_M2_0706_P", + "Mouse Kidney M430v2 (Jul06) PDNN" + ], + [ + "MA_M2_0706_R", + "Mouse Kidney M430v2 (Jul06) RMA" ] ], - "Phenotypes": [ + "Leucocytes": [ [ - "LXSPublish", - "LXS Published Phenotypes" + "Illum_BXD_PBL_1108", + "UWA Illumina PBL (Nov08) RSN **" ] ], - "Prefrontal Cortex": [ + "Liver": [ [ - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" + "GSE16780_UCLA_ML0911", + "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" ], [ - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" + "GenEx_BXD_liverSal_RMA_F_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" + ], + [ + "GenEx_BXD_liverSal_RMA_M_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" + ], + [ + "GenEx_BXD_liverSal_RMA_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + ], + [ + "GenEx_BXD_liverEt_RMA_F_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" + ], + [ + "GenEx_BXD_liverEt_RMA_M_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" + ], + [ + "GenEx_BXD_liverEt_RMA_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + ], + [ + "SUH_Liv_RMA_0611", + "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" + ] + ], + "Lung": [ + [ + "HZI_0408_R", + "HZI Lung M430v2 (Apr08) RMA" + ], + [ + "HZI_0408_M", + "HZI Lung M430v2 (Apr08) MAS5" + ] + ], + "Midbrain": [ + [ + "VUBXDMouseMidBrainQ0212", + "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (Feb12) Quantile" + ] + ], + "Muscle": [ + [ + "EPFLMouseMuscleRMA1211", + "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + ], + [ + "EPFLMouseMuscleHFDRMA1211", + "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + ], + [ + "EPFLMouseMuscleCDRMA1211", + "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + ] + ], + "Neocortex": [ + [ + "DevNeocortex_ILM6.2P14RInv_1111", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv **" + ], + [ + "DevNeocortex_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv **" + ], + [ + "HQFNeoc_1210v2_RankInv", + "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" + ], + [ + "HQFNeoc_1210_RankInv", + "HQF BXD Neocortex ILM6v1.1 (Dec10) RankInv" ], [ - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" + "HQFNeoc_0208_RankInv", + "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" ], [ - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" + "DevNeocortex_ILM6.2P3RInv_1110", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv **" ], [ - "INIA_MacFas_Pf_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex control (Jan10) RMA **" - ], + "DevNeocortex_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv **" + ] + ], + "Nucleus Accumbens": [ [ - "INIA_MacFas_PfE_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex ethanol (Jan10) RMA **" + "VCUSalo_1007_R", + "VCU BXD NA Sal M430 2.0 (Oct07) RMA" ], [ - "VCUSal_1006_R", - "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + "VCUEtOH_1007_R", + "VCU BXD NA EtOH M430 2.0 (Oct07) RMA **" ], + [ + "VCUSal_1007_R", + "VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore **" + ] + ], + "Phenotypes": [ + [ + "BXDPublish", + "BXD Published Phenotypes" + ] + ], + "Prefrontal Cortex": [ [ "VCUEtOH_1206_R", "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" @@ -5035,6 +1275,10 @@ "VCUSal_1206_R", "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" ], + [ + "VCUSal_1006_R", + "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + ], [ "VCU_PF_Air_0111_R", "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" @@ -5046,365 +1290,347 @@ [ "VCU_PF_AvE_0111_Ss", "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" - ], - [ - "VCUEt_vs_Sal_0806_R", - "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" - ], - [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], - [ - "VCUSal_0806_R", - "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" - ] - ] - }, - "MDP": { - "Genotypes": [ - [ - "MDPGeno", - "MDP Genotypes" ] ], - "Hippocampus": [ - [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], - [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], + "Retina": [ [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" + "Illum_Retina_BXD_RankInv0410", + "HEI Retina Illumina V6.2 (April 2010) RankInv" ], [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" + "B6D2ONCILM_0412", + "B6D2 ONC Illumina v6.1 (Apr12) RankInv **" ], [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" + "ONCRetILM6_0412", + "ONC Retina Illumina V6.2 (Apr12) RankInv **" ], [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" + "HEIONCvsCRetILM6_0911", + "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" ], [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" + "G2HEIONCRetILM6_0911", + "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" ], [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" + "HEIONCRetILM6_0911", + "HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" ], [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" + "ILM_Retina_BXD_F_RankInv1210", + "HEI Retina Females Illumina V6.2 (Dec10) RankInv **" ], [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" + "ILM_Retina_BXD_M_RankInv1210", + "HEI Retina Males Illumina V6.2 (Dec10) RankInv **" ], [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" + "ILM_Retina_BXD_FM_RankInv1210", + "HEI Retina F-M Illumina V6.2 (Dec10) RankInv **" ], [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" - ], + "G2NEI_ILM_Retina_BXD_RI0410", + "G2NEI Retina Illumina V6.2 (April 2010) RankInv **" + ] + ], + "Spleen": [ [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" + "UTHSC_SPL_RMA_1210", + "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" ], [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" + "UTHSC_SPL_RMA_1010", + "UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA" ], [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" + "IoP_SPL_RMA_0509", + "IoP Affy MOE 430v2 Spleen (May09) RMA" ], [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" + "Illum_BXD_Spl_1108", + "UWA Illumina Spleen (Nov08) RSN **" ], [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], + "UTK_BXDSpl_VST_0110", + "UTK Spleen ILM6.1 (Jan10) VST" + ] + ], + "Striatum": [ [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" + "DevStriatum_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" ], [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" + "DevStriatum_ILM6.2P14RInv_1111", + "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" ], [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" + "UTHSC_Striatum_RankInv_1210", + "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" ], [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" + "UTHSC_Str_RankInv_1210", + "HQF BXD Striatum ILM6.1 (Dec10) RankInv" ], [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" + "UTHSC_1107_RankInv", + "HQF BXD Striatum ILM6.1 (Nov07) RankInv" ], [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" + "SA_M2_0405_MC", + "HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean" ], [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" + "SA_M2_0405_RC", + "HBP Rosen Striatum M430V2 (Apr05) RMA Clean" ], [ - "UT_ILM_BXD_hipp_RSE_0909", - "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" + "SA_M2_0405_PC", + "HBP Rosen Striatum M430V2 (Apr05) PDNN Clean" ], [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" + "SA_M2_0405_SS", + "HBP Rosen Striatum M430V2 (Apr05) SScore" ], [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" + "SA_M2_0405_RR", + "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" ], [ - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" + "Striatum_Exon_0209", + "HQF Striatum Exon (Feb09) RMA" ], [ - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" + "DevStriatum_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" ], [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" + "DevStriatum_ILM6.2P3RInv_1110", + "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" ] ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "JAX_CSB_L_0711", - "JAX Liver Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_HF_0711", - "JAX Liver HF Affy M430 2.0 (Jul11) MDP" - ], - [ - "JAX_CSB_L_6C_0711", - "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], + "T Cell (helper)": [ [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], + "RTHC_0211_R", + "HZI Thelp M430v2 (Feb11) RMA" + ] + ], + "T Cell (regulatory)": [ [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], + "RTC_1106_R", + "HZI Treg M430v2 (Feb11) RMA" + ] + ], + "Thymus": [ [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], + "Illum_BXD_Thy_1108", + "UWA Illumina Thymus (Nov08) RSN **" + ] + ], + "Ventral Tegmental Area": [ [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" + "VCUEtOH_0609_R", + "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" ], [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" + "VCUSal_0609_R", + "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" ], [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], + "VCUEtvsSal_0609_R", + "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **" + ] + ] + }, + "BXH": { + "Cartilage": [ [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" + "UCLA_BXHBXD_CARTILAGE_V2", + "UCLA BXH and BXD Cartilage v2" ], [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" + "UCLA_BXHBXD_CARTILAGE", + "UCLA BXH and BXD Cartilage" ], [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], + "UCLA_BXH_CARTILAGE", + "UCLA BXH Cartilage" + ] + ], + "Genotypes": [ [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ], + "BXHGeno", + "BXH Genotypes" + ] + ], + "Phenotypes": [ [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], + "BXHPublish", + "BXH Published Phenotypes" + ] + ] + }, + "CTB6F2": { + "Adipose": [ [ - "HXB_Liver_1208", - "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" + "UCLA_CTB6B6CTF2_ADIPOSE_MALE", + "UCLA CTB6B6CTF2 Adipose Male mlratio **" ], [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" + "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE", + "UCLA CTB6B6CTF2 Adipose Female mlratio **" ], [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], + "UCLA_CTB6B6CTF2_ADIPOSE_2005", + "UCLA CTB6/B6CTF2 Adipose (2005) mlratio **" + ] + ], + "Brain": [ [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" + "UCLA_CTB6B6CTF2_BRAIN_MALE", + "UCLA CTB6B6CTF2 Brain Male mlratio **" ], [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" + "UCLA_CTB6B6CTF2_BRAIN_FEMALE", + "UCLA CTB6B6CTF2 Brain Female mlratio **" ], [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], + "UCLA_CTB6B6CTF2_BRAIN_2005", + "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" + ] + ], + "Genotypes": [ [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" + "CTB6F2Geno", + "CTB6F2 Genotypes" + ] + ], + "Liver": [ + [ + "UCLA_CTB6B6CTF2_LIVER_MALE", + "UCLA CTB6B6CTF2 Liver Male mlratio **" ], [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" + "UCLA_CTB6B6CTF2_LIVER_FEMALE", + "UCLA CTB6B6CTF2 Liver Female mlratio **" ], [ "UCLA_CTB6B6CTF2_LIVER_2005", "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], + ] + ], + "Muscle": [ [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" + "UCLA_CTB6B6CTF2_MUSCLE_MALE", + "UCLA CTB6B6CTF2 Muscle Male mlratio **" ], [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" + "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", + "UCLA CTB6B6CTF2 Muscle Female mlratio **" ], [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" + "UCLA_CTB6B6CTF2_MUSCLE_2005", + "UCLA CTB6/B6CTF2 Muscle (2005) mlratio **" ] ], "Phenotypes": [ [ - "MDPPublish", - "Mouse Phenome Database" + "CTB6F2Publish", + "CTB6F2 Published Phenotypes" ] ] }, - "NZBXFVB-N2": { + "CXB": { "Genotypes": [ [ - "NZBXFVB-N2Geno", - "NZBXFVB-N2 Genotypes" + "CXBGeno", + "CXB Genotypes" ] ], - "Mammary Tumors": [ - [ - "NCI_Mam_Tum_RMA_0409", - "NCI Mammary M430v2 (Apr09) RMA" - ], - [ - "NCI_Agil_Mam_Tum_RMA_0409", - "NCI Mammary LMT miRNA v2 (Apr09) RMA" - ], + "Hippocampus": [ [ - "MA_M_0704_R", - "NCI Mammary mRNA M430 (July04) RMA" + "HC_M2CB_1205_R", + "Hippocampus Consortium M430v2 CXB (Dec05) RMA" ], [ - "MA_M_0704_M", - "NCI Mammary mRNA M430 (July04) MAS5" + "HC_M2CB_1205_P", + "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" ] ], "Phenotypes": [ [ - "NZBXFVB-N2Publish", - "NZBXFVB-N2 Published Phenotypes" + "CXBPublish", + "CXB Published Phenotypes" ] - ] - } - }, - "rat": { - "HXBBXH": { - "Adrenal Gland": [ + ], + "Spleen": [ [ - "HXB_Adrenal_1208", - "MDC/CAS/UCL Adrenal 230A (Dec08) RMA" + "STSPL_1107_R", + "Stuart Spleen M430v2 (Nov07) RMA" ] - ], + ] + }, + "HS": { "Genotypes": [ [ - "HXBBXHGeno", - "HXBBXH Genotypes" + "HSGeno", + "HS Genotypes" ] ], - "Heart": [ + "Hippocampus": [ [ - "HXB_Heart_1208", - "MDC/CAS/UCL Heart 230_V2 (Dec08) RMA" + "OXUKHS_ILMHipp_RI0510", + "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" ] ], - "Hippocampus": [ + "Liver": [ [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ], + "OXUKHS_ILMLiver_RI0510", + "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" + ] + ], + "Lung": [ [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], + "OXUKHS_ILMLung_RI0510", + "OX UK HS ILM6v1.1 Lung (May 2010) RankInv" + ] + ], + "Phenotypes": [ [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], + "HSPublish", + "HS Published Phenotypes" + ] + ] + }, + "HS-CC": { + "Genotypes": [ [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" - ], + "HS-CCGeno", + "HS-CC Genotypes" + ] + ], + "Phenotypes": [ [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" - ], + "HS-CCPublish", + "HS-CC Published Phenotypes" + ] + ], + "Striatum": [ [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" - ], + "OHSU_HS-CC_ILMStr_0211", + "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" + ] + ] + }, + "LXS": { + "Genotypes": [ [ - "UT_HippRatEx_RMA_0709", - "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" - ], + "LXSGeno", + "LXS Genotypes" + ] + ], + "Hippocampus": [ [ "Illum_LXS_Hipp_loess0807", "Hippocampus Illumina (Aug07) LOESS" @@ -5426,65 +1652,25 @@ "Hippocampus Illumina (Aug07) RSN" ], [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" - ], - [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" - ], - [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" - ], - [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" - ], - [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], - [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" + "Illum_LXS_Hipp_rsn_nb0807", + "Hippocampus Illumina (Aug07) RSN_NB" ], [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" + "Hipp_Illumina_RankInv_0507", + "Hippocampus Illumina (May07) RankInv" ], [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" + "Illum_LXS_Hipp_NOS_1008", + "Hippocampus Illumina NOS (Oct08) RankInv beta" ], [ - "UT_ILM_BXD_hipp_RSE_0909", - "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" + "Illum_LXS_Hipp_NON_1008", + "Hippocampus Illumina NON (Oct08) RankInv beta" ], [ "Illum_LXS_Hipp_RSE_1008", "Hippocampus Illumina RSE (Oct08) RankInv beta" ], - [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], [ "Illum_LXS_Hipp_NOE_1008", "Hippocampus Illumina NOE (Oct08) RankInv beta" @@ -5492,55 +1678,47 @@ [ "Illum_LXS_Hipp_RSS_1008", "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" ] ], - "Kidney": [ - [ - "MA_M2F_0706_R", - "Mouse kidney M430v2 Female (Aug06) RMA" - ], - [ - "MA_M2M_0706_R", - "Mouse kidney M430v2 Male (Aug06) RMA" - ], + "Phenotypes": [ [ - "MA_M2_0806_R", - "Mouse kidney M430v2 Sex Balanced (Aug06) RMA" - ], + "LXSPublish", + "LXS Published Phenotypes" + ] + ], + "Prefrontal Cortex": [ [ - "MA_M2_0806_P", - "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" ], [ - "MA_M2_0706_P", - "Mouse Kidney M430v2 (Jul06) PDNN" + "VCUSal_0806_R", + "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" ], [ - "MA_M2_0706_R", - "Mouse Kidney M430v2 (Jul06) RMA" - ], + "VCUEt_vs_Sal_0806_R", + "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" + ] + ] + }, + "MDP": { + "Genotypes": [ [ - "KI_2A_0405_M", - "MDC/CAS/ICL Kidney 230A (Apr05) MAS5" - ], + "MDPGeno", + "MDP Genotypes" + ] + ], + "Hippocampus": [ [ - "KI_2A_0405_Rz", - "MDC/CAS/ICL Kidney 230A (Apr05) RMA 2z+8" + "UMUTAffyExon_0209_RMA_MDP", + "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" ], [ - "KI_2A_0405_R", - "MDC/CAS/ICL Kidney 230A (Apr05) RMA" + "HC_M2_0606_MDP", + "Hippocampus Consortium M430v2 (Jun06) RMA MDP" ] ], "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], [ "JAX_CSB_L_0711", "JAX Liver Affy M430 2.0 (Jul11) MDP" @@ -5552,114 +1730,80 @@ [ "JAX_CSB_L_6C_0711", "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" - ], - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], + ] + ], + "Phenotypes": [ [ - "LV_G_0106_F", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females" - ], + "MDPPublish", + "Mouse Phenome Database" + ] + ] + }, + "NZBXFVB-N2": { + "Genotypes": [ [ - "LV_G_0106_M", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males" - ], + "NZBXFVB-N2Geno", + "NZBXFVB-N2 Genotypes" + ] + ], + "Mammary Tumors": [ [ - "LV_G_0106_B", - "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes" - ], + "NCI_Mam_Tum_RMA_0409", + "NCI Mammary M430v2 (Apr09) RMA" + ] + ], + "Phenotypes": [ [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], + "NZBXFVB-N2Publish", + "NZBXFVB-N2 Published Phenotypes" + ] + ] + } + }, + "rat": { + "HXBBXH": { + "Adrenal Gland": [ [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], + "HXB_Adrenal_1208", + "MDC/CAS/UCL Adrenal 230A (Dec08) RMA" + ] + ], + "Genotypes": [ [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], + "HXBBXHGeno", + "HXBBXH Genotypes" + ] + ], + "Heart": [ [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], + "HXB_Heart_1208", + "MDC/CAS/UCL Heart 230_V2 (Dec08) RMA" + ] + ], + "Hippocampus": [ [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], + "UT_HippRatEx_RMA_0709", + "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" + ] + ], + "Kidney": [ [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + "KI_2A_0405_M", + "MDC/CAS/ICL Kidney 230A (Apr05) MAS5" ], [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" + "KI_2A_0405_Rz", + "MDC/CAS/ICL Kidney 230A (Apr05) RMA 2z+8" ], [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ], + "KI_2A_0405_R", + "MDC/CAS/ICL Kidney 230A (Apr05) RMA" + ] + ], + "Liver": [ [ "HXB_Liver_1208", "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ], - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ], - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" ] ], "Peritoneal Fat": [ @@ -5681,38 +1825,6 @@ }, "SRxSHRSPF2": { "Eye": [ - [ - "Eye_AXBXA_1008_RankInv", - "Eye AXBXA Illumina V6.2(Oct08) RankInv Beta" - ], - [ - "Eye_M2_0908_R", - "Eye M430v2 (Sep08) RMA" - ], - [ - "Eye_M2_0908_R_NB", - "Eye M430v2 Mutant Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_ND", - "Eye M430v2 WT Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_WTWT", - "Eye M430v2 WT WT (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" - ], - [ - "BXD_GLA_0911", - "BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **" - ], [ "UIOWA_Eye_RMA_0906", "UIOWA Eye mRNA RAE230v2 (Sep06) RMA" diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index e7e260fe..d639ed07 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -23,6 +23,10 @@ from base import webqtlFormData from pprint import pformat as pf +#import logging +#logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO) +#_log = logging.getLogger("correlation") + @app.route("/") def index_page(): @@ -33,7 +37,7 @@ def index_page(): @app.route("/new") def new_index_page(): print("Sending index_page") - + return render_template("new_index_page.html") @app.route("/data_sharing") @@ -54,6 +58,7 @@ def data_sharing_page(): @app.route("/search") def search_page(): + print("in search_page") if 'info_database' in request.args: print("Going to sharing_info_page") template_vars = sharing_info_page() @@ -63,7 +68,9 @@ def search_page(): else: return render_template("data_sharing.html", **template_vars.__dict__) else: + print("calling search_results.SearchResultPage") the_search = search_results.SearchResultPage(request.args) + print("done calling") return render_template("search_result_page.html", **the_search.__dict__) -- cgit v1.2.3 From a3e23950f25863697128eb3e40fd346c848e7ae5 Mon Sep 17 00:00:00 2001 From: Zachary Sloan Date: Thu, 25 Oct 2012 15:48:14 -0500 Subject: Got the Make Default option working on the home page --- wqflask/cfg/default_settings.py | 4 + wqflask/cfg/zach_settings.py | 1 + wqflask/maintenance/gen_select_dataset.py | 33 +- .../static/new/javascript/dataset_menu_structure | 2904 -------------------- .../static/new/javascript/dataset_select_items.js | 773 ------ .../new/javascript/dataset_select_menu.coffee | 10 +- .../static/new/javascript/dataset_select_menu.js | 12 +- 7 files changed, 46 insertions(+), 3691 deletions(-) delete mode 100644 wqflask/wqflask/static/new/javascript/dataset_menu_structure delete mode 100755 wqflask/wqflask/static/new/javascript/dataset_select_items.js (limited to 'wqflask/maintenance/gen_select_dataset.py') diff --git a/wqflask/cfg/default_settings.py b/wqflask/cfg/default_settings.py index 30ad51d1..1811ccfd 100644 --- a/wqflask/cfg/default_settings.py +++ b/wqflask/cfg/default_settings.py @@ -1 +1,5 @@ LOGFILE = """/tmp/flask_gn_log""" + +#This is needed because Flask turns key errors into a +#400 bad request response with no exception/log +TRAP_BAD_REQUEST_ERRORS = True diff --git a/wqflask/cfg/zach_settings.py b/wqflask/cfg/zach_settings.py index 30ad51d1..ed97f222 100644 --- a/wqflask/cfg/zach_settings.py +++ b/wqflask/cfg/zach_settings.py @@ -1 +1,2 @@ LOGFILE = """/tmp/flask_gn_log""" +TRAP_BAD_REQUEST_ERRORS = True diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 9224b884..4c544192 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -1,3 +1,10 @@ +"""Script that generates the data for the main dropdown menus on the home page + +Writes out data as /static/new/javascript/dataset_menu_structure.json +It needs to be run manually when database has been changed. + +""" + # Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it @@ -13,16 +20,13 @@ # This program is available from Source Forge: at GeneNetwork Project # (sourceforge.net/projects/genenetwork/). # -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# Contact Drs. Robert W. Williams +# at rwilliams@uthsc.edu # # # # This module is used by GeneNetwork project (www.genenetwork.org) -# This script is to generate the data for the main menus on the home page -# It needs to be run manually when database has been changed . - from __future__ import print_function, division import sys @@ -39,7 +43,8 @@ from base import webqtlConfig # build MySql database connection -Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, +Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, + host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD) Cursor = Con.cursor() @@ -82,6 +87,12 @@ def get_types(groups): def build_types(species, group): + """Fetches tissues + + Gets the tissues with data for this species/group + (all types except phenotype/genotype are tissues) + + """ Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and @@ -101,12 +112,13 @@ def get_datasets(types): datasets[species] = {} for group, type_list in group_dict.iteritems(): datasets[species][group] = {} - for type_name, type_full_name in type_list: + for type_name, _type_full_name in type_list: datasets[species][group][type_name] = build_datasets(species, group, type_name) return datasets def build_datasets(species, group, type_name): + """Gets dataset names from database""" dataset_text = dataset_value = None if type_name == "Phenotypes": dataset_value = "%sPublish" % group @@ -135,6 +147,7 @@ def build_datasets(species, group, type_name): def main(): + """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" species = get_species() groups = get_groups(species) types = get_types(groups) @@ -154,14 +167,16 @@ def main(): datasets=datasets, ) - output_file = """../wqflask/static/new/javascript/dataset_menu_structure""" + output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json""" with open(output_file, 'w') as fh: json.dump(data, fh, indent=" ", sort_keys=True) print("\nWrote file to:", output_file) -def test_it(): + +def _test_it(): + """Used for internal testing only""" types = build_types("Mouse", "BXD") print("build_types:", pf(types)) datasets = build_datasets("Mouse", "BXD", "Hippocampus") diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure b/wqflask/wqflask/static/new/javascript/dataset_menu_structure deleted file mode 100644 index 1b7e4090..00000000 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure +++ /dev/null @@ -1,2904 +0,0 @@ -{ - "datasets": { - "All Species": { - "All Groups": { - "Phenotypes": [ - [ - "All Phenotypes", - "All Phenotypes" - ] - ] - } - }, - "arabidopsis": { - "BayXSha": { - "Genotypes": [ - [ - "BayXShaGeno", - "BayXSha Genotypes" - ] - ], - "Phenotypes": [ - [ - "BayXShaPublish", - "BayXSha Published Phenotypes" - ] - ] - }, - "ColXBur": { - "Genotypes": [ - [ - "ColXBurGeno", - "ColXBur Genotypes" - ] - ], - "Phenotypes": [ - [ - "ColXBurPublish", - "ColXBur Published Phenotypes" - ] - ] - }, - "ColXCvi": { - "Genotypes": [ - [ - "ColXCviGeno", - "ColXCvi Genotypes" - ] - ], - "Phenotypes": [ - [ - "ColXCviPublish", - "ColXCvi Published Phenotypes" - ] - ] - } - }, - "barley": { - "QSM": { - "Genotypes": [ - [ - "QSMGeno", - "QSM Genotypes" - ] - ], - "Leaf": [ - [ - "B1LI0809R", - "Barley1 Leaf INOC TTKS (Aug09) RMA" - ], - [ - "B1LI0809M5", - "Barley1 Leaf INOC TTKS (Aug09) MAS5" - ], - [ - "B1MI0809M5", - "Barley1 Leaf MOCK TTKS (Aug09) MAS5" - ], - [ - "B1MI0809R", - "Barley1 Leaf MOCK TTKS (Aug09) RMA" - ] - ], - "Phenotypes": [ - [ - "QSMPublish", - "QSM Published Phenotypes" - ] - ] - }, - "SXM": { - "Embryo": [ - [ - "B139_K_1206_R", - "Barley1 Embryo gcRMA SCRI (Dec06)" - ], - [ - "B139_K_1206_M", - "Barley1 Embryo MAS 5.0 SCRI (Dec06)" - ], - [ - "B150_K_0406_R", - "Barley1 Embryo0 gcRMA SCRI (Apr06)" - ] - ], - "Genotypes": [ - [ - "SXMGeno", - "SXM Genotypes" - ] - ], - "Leaf": [ - [ - "B30_K_1206_M", - "Barley1 Leaf MAS 5.0 SCRI (Dec06)" - ], - [ - "B30_K_1206_Rn", - "Barley1 Leaf gcRMAn SCRI (Dec06)" - ], - [ - "B30_K_1206_R", - "Barley1 Leaf gcRMA SCRI (Dec06)" - ] - ], - "Phenotypes": [ - [ - "SXMPublish", - "SXM Published Phenotypes" - ] - ] - } - }, - "drosophila": { - "DGRP": { - "Genotypes": [ - [ - "DGRPGeno", - "DGRP Genotypes" - ] - ], - "Phenotypes": [ - [ - "DGRPPublish", - "DGRP Published Phenotypes" - ] - ], - "Whole Body": [ - [ - "NCSU_DrosWB_LC_RMA_0111", - "NCSU Drosophila Whole Body (Jan11) RMA" - ] - ] - }, - "Oregon-R_x_2b3": { - "Genotypes": [ - [ - "Oregon-R_x_2b3Geno", - "Oregon-R_x_2b3 Genotypes" - ] - ], - "Phenotypes": [ - [ - "Oregon-R_x_2b3Publish", - "Oregon-R_x_2b3 Published Phenotypes" - ] - ], - "Whole Body": [ - [ - "UAB_DrosWB_LC_RMA_1009", - "UAB Whole body D.m. mRNA control (Oct09) RMA" - ], - [ - "UAB_DrosWB_LE_RMA_1009", - "UAB Whole body D.m. mRNA lead (pbAc) (Oct09) RMA" - ] - ] - } - }, - "human": { - "AD-cases-controls": { - "Brain": [ - [ - "GSE5281_F_RMA_N_0709", - "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA_Alzh_0709", - "GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA" - ], - [ - "GSE5281_F_RMA0709", - "GSE5281 Human Brain Full Liang (Jul09) RMA" - ], - [ - "GSE5281_RMA0709", - "GSE5281 Human Brain Best 102 Liang (Jul09) RMA" - ] - ], - "Genotypes": [ - [ - "AD-cases-controlsGeno", - "AD-cases-controls Genotypes" - ] - ], - "Phenotypes": [ - [ - "AD-cases-controlsPublish", - "AD-cases-controls Published Phenotypes" - ] - ] - }, - "AD-cases-controls-Myers": { - "Brain": [ - [ - "GSE15222_F_A_RI_0409", - "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], - [ - "GSE15222_F_RI_0409", - "GSE15222 Human Brain Myers (Apr09) RankInv" - ] - ], - "Genotypes": [ - [ - "AD-cases-controls-MyersGeno", - "AD-cases-controls-Myers Genotypes" - ] - ], - "Phenotypes": [ - [ - "AD-cases-controls-MyersPublish", - "AD-cases-controls-Myers Published Phenotypes" - ] - ] - }, - "CANDLE": { - "Genotypes": [ - [ - "CANDLEGeno", - "CANDLE Genotypes" - ] - ], - "Newborn Cord Blood": [ - [ - "CANDLE_NB_0711", - "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT **" - ] - ], - "Phenotypes": [ - [ - "CANDLEPublish", - "CANDLE Published Phenotypes" - ] - ] - }, - "CEPH-2004": { - "Genotypes": [ - [ - "CEPH-2004Geno", - "CEPH-2004 Genotypes" - ] - ], - "Lymphoblast B-cell": [ - [ - "UT_CEPH_RankInv0909", - "UTHSC CEPH B-cells Illumina (Sep09) RankInv" - ], - [ - "Human_1008", - "Monks CEPH B-cells Agilent (Dec04) Log10Ratio" - ] - ], - "Phenotypes": [ - [ - "CEPH-2004Publish", - "CEPH-2004 Published Phenotypes" - ] - ] - }, - "HB": { - "Cerebellum": [ - [ - "HBTRC-MLC_0611", - "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLC_N_0611", - "HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLC_AD_0611", - "HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLC_HD_0611", - "HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio" - ] - ], - "Genotypes": [ - [ - "HBGeno", - "HB Genotypes" - ] - ], - "Phenotypes": [ - [ - "HBPublish", - "HB Published Phenotypes" - ] - ], - "Prefrontal Cortex": [ - [ - "HBTRC-MLPFC_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_N_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_AD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLPFC_HD_0611", - "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" - ] - ], - "Primary Visual Cortex": [ - [ - "HBTRC-MLVC_0611", - "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_N_0611", - "HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_AD_0611", - "HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio" - ], - [ - "HBTRC-MLVC_HD_0611", - "HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio" - ] - ] - }, - "HLC": { - "Genotypes": [ - [ - "HLCGeno", - "HLC Genotypes" - ] - ], - "Liver": [ - [ - "HLC_0311", - "GSE9588 Human Liver Normal (Mar11) Both Sexes" - ], - [ - "HLCM_0311", - "GSE9588 Human Liver Normal (Mar11) Males" - ], - [ - "HLCF_0311", - "GSE9588 Human Liver Normal (Mar11) Females" - ] - ], - "Phenotypes": [ - [ - "HLCPublish", - "HLC Published Phenotypes" - ] - ] - }, - "HSB": { - "Amygdala": [ - [ - "KIN_YSM_AMY_0711", - "KIN/YSM Human AMY Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Caudal Ganglionic Eminence": [ - [ - "KIN_YSM_CGE_0711", - "KIN/YSM Human CGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Cerebellar Cortex": [ - [ - "KIN_YSM_CBC_0711", - "KIN/YSM Human CBC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Diencephalon": [ - [ - "KIN_YSM_DIE_0711", - "KIN/YSM Human DIE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Dorsal Thalamus": [ - [ - "KIN_YSM_DTH_0711", - "KIN/YSM Human DTH Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Dorsolateral Prefrontal Cortex": [ - [ - "KIN_YSM_DFC_0711", - "KIN/YSM Human DFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Frontal Cerebral Wall": [ - [ - "KIN_YSM_FC_0711", - "KIN/YSM Human FC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Genotypes": [ - [ - "HSBGeno", - "HSB Genotypes" - ] - ], - "Hippocampus": [ - [ - "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Inferior Temporal Cortex": [ - [ - "KIN_YSM_ITC_0711", - "KIN/YSM Human ITC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Lateral Ganglionic Eminence": [ - [ - "KIN_YSM_LGE_0711", - "KIN/YSM Human LGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Medial Ganglionic Eminence": [ - [ - "KIN_YSM_MGE_0711", - "KIN/YSM Human MGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Medial Prefrontal Cortex": [ - [ - "KIN_YSM_MFC_0711", - "KIN/YSM Human MFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Mediodorsal Nucleus of Thalamus": [ - [ - "KIN_YSM_MD_0711", - "KIN/YSM Human MD Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Occipital Cerebral Wall": [ - [ - "KIN_YSM_OC_0711", - "KIN/YSM Human OC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Orbital Prefrontal Cortex": [ - [ - "KIN_YSM_OFC_0711", - "KIN/YSM Human OFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Parietal Cerebral Wall": [ - [ - "KIN_YSM_PC_0711", - "KIN/YSM Human PC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Phenotypes": [ - [ - "HSBPublish", - "HSB Published Phenotypes" - ] - ], - "Posterior Inferior Parietal Cortex": [ - [ - "KIN_YSM_IPC_0711", - "KIN/YSM Human IPC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Posterior Superior Temporal Cortex": [ - [ - "KIN_YSM_STC_0711", - "KIN/YSM Human STC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Auditory (A1) Cortex": [ - [ - "KIN_YSM_A1C_0711", - "KIN/YSM Human A1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Motor (M1) Cortex": [ - [ - "KIN_YSM_M1C_0711", - "KIN/YSM Human M1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Somatosensory (S1) Cortex": [ - [ - "KIN_YSM_S1C_0711", - "KIN/YSM Human S1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Primary Visual Cortex": [ - [ - "KIN_YSM_V1C_0711", - "KIN/YSM Human V1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Striatum": [ - [ - "KIN_YSM_STR_0711", - "KIN/YSM Human STR Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Temporal Cerebral Wall": [ - [ - "KIN_YSM_TC_0711", - "KIN/YSM Human TC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Upper (Rostral) Rhombic Lip": [ - [ - "KIN_YSM_URL_0711", - "KIN/YSM Human URL Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Ventral Forebrain": [ - [ - "KIN_YSM_VF_0711", - "KIN/YSM Human VF Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ], - "Ventrolateral Prefrontal Cortex": [ - [ - "KIN_YSM_VFC_0711", - "KIN/YSM Human VFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" - ] - ] - } - }, - "macaque monkey": { - "Macaca-fasicularis": { - "Amygdala": [ - [ - "INIA_MacFas_AMGc_RMA_0110", - "INIA Macaca fasicularis Amygdala control (Jan10) RMA **" - ], - [ - "INIA_MacFas_AMGe_RMA_0110", - "INIA Macaca fasicularis Amygdala ethanol (Jan10) RMA **" - ] - ], - "Brain": [ - [ - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ] - ], - "Genotypes": [ - [ - "Macaca-fasicularisGeno", - "Macaca-fasicularis Genotypes" - ] - ], - "Hippocampus": [ - [ - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus control (Jan10) RMA **" - ], - [ - "INIA_MacFas_He_RMA_0110", - "INIA Macaca fasicularis Hippocampus ethanol (Jan10) RMA **" - ] - ], - "Nucleus Accumbens": [ - [ - "INIA_MacFas_Ac_RMA_0110", - "INIA Macaca fasicularis Nucleus Accumbens control (Jan10) RMA **" - ], - [ - "INIA_MacFas_Ae_RMA_0110", - "INIA Macaca fasicularis Nucleus Accumbens ethanol (Jan10) RMA **" - ] - ], - "Phenotypes": [ - [ - "Macaca-fasicularisPublish", - "Macaca-fasicularis Published Phenotypes" - ] - ], - "Prefrontal Cortex": [ - [ - "INIA_MacFas_Pf_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex control (Jan10) RMA **" - ], - [ - "INIA_MacFas_PfE_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex ethanol (Jan10) RMA **" - ] - ] - } - }, - "mouse": { - "AKXD": { - "Genotypes": [ - [ - "AKXDGeno", - "AKXD Genotypes" - ] - ], - "Mammary Tumors": [ - [ - "NCI_Agil_Mam_Tum_RMA_0409", - "NCI Mammary LMT miRNA v2 (Apr09) RMA" - ], - [ - "MA_M_0704_R", - "NCI Mammary mRNA M430 (July04) RMA" - ], - [ - "MA_M_0704_M", - "NCI Mammary mRNA M430 (July04) MAS5" - ] - ], - "Phenotypes": [ - [ - "AKXDPublish", - "AKXD Published Phenotypes" - ] - ] - }, - "AXBXA": { - "Eye": [ - [ - "Eye_AXBXA_1008_RankInv", - "Eye AXBXA Illumina V6.2(Oct08) RankInv Beta" - ] - ], - "Genotypes": [ - [ - "AXBXAGeno", - "AXBXA Genotypes" - ] - ], - "Phenotypes": [ - [ - "AXBXAPublish", - "AXBXA Published Phenotypes" - ] - ] - }, - "B6BTBRF2": { - "Genotypes": [ - [ - "B6BTBRF2Geno", - "B6BTBRF2 Genotypes" - ] - ], - "Liver": [ - [ - "LVF2_M_0704_R", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" - ], - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ] - ], - "Phenotypes": [ - [ - "B6BTBRF2Publish", - "B6BTBRF2 Published Phenotypes" - ] - ] - }, - "B6D2F2": { - "Brain": [ - [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ - "BRF2_M_0805_M", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" - ], - [ - "BRF2_M_0805_P", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" - ], - [ - "BRF2_M_0304_P", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" - ], - [ - "BRF2_M_0304_R", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" - ], - [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ] - ], - "Genotypes": [ - [ - "B6D2F2Geno", - "B6D2F2 Genotypes" - ] - ], - "Phenotypes": [ - [ - "B6D2F2Publish", - "B6D2F2 Published Phenotypes" - ] - ] - }, - "BDF2-1999": { - "Genotypes": [ - [ - "BDF2-1999Geno", - "BDF2-1999 Genotypes" - ] - ], - "Liver": [ - [ - "UCLA_BDF2_LIVER_1999", - "UCLA BDF2 Liver (1999) mlratio" - ] - ], - "Phenotypes": [ - [ - "BDF2-1999Publish", - "BDF2-1999 Published Phenotypes" - ] - ] - }, - "BDF2-2005": { - "Genotypes": [ - [ - "BDF2-2005Geno", - "BDF2-2005 Genotypes" - ] - ], - "Phenotypes": [ - [ - "BDF2-2005Publish", - "BDF2-2005 Published Phenotypes" - ] - ], - "Striatum": [ - [ - "SA_M2_0905_R", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" - ], - [ - "SA_M2_0905_M", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" - ], - [ - "SA_M2_0905_P", - "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN" - ] - ] - }, - "BHF2": { - "Adipose": [ - [ - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], - [ - "UCLA_BHF2_ADIPOSE_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], - [ - "UCLA_BHF2_ADIPOSE_0605", - "UCLA BHF2 Adipose (June05) mlratio" - ] - ], - "Brain": [ - [ - "UCLA_BHF2_BRAIN_MALE", - "UCLA BHF2 Brain Male mlratio" - ], - [ - "UCLA_BHF2_BRAIN_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], - [ - "UCLA_BHF2_BRAIN_0605", - "UCLA BHF2 Brain (June05) mlratio" - ] - ], - "Genotypes": [ - [ - "BHF2Geno", - "BHF2 Genotypes" - ] - ], - "Liver": [ - [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], - [ - "UCLA_BHF2_LIVER_0605", - "UCLA BHF2 Liver (June05) mlratio" - ] - ], - "Muscle": [ - [ - "UCLA_BHF2_MUSCLE_MALE", - "UCLA BHF2 Muscle Male mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], - [ - "UCLA_BHF2_MUSCLE_0605", - "UCLA BHF2 Muscle (June05) mlratio **" - ] - ], - "Phenotypes": [ - [ - "BHF2Publish", - "BHF2 Published Phenotypes" - ] - ] - }, - "BHHBF2": { - "Adipose": [ - [ - "UCLA_BHHBF2_ADIPOSE_MALE", - "UCLA BHHBF2 Adipose Male Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_FEMALE", - "UCLA BHHBF2 Adipose Female Only" - ], - [ - "UCLA_BHHBF2_ADIPOSE_2005", - "UCLA BHHBF2 Adipose (2005) mlratio **" - ] - ], - "Brain": [ - [ - "UCLA_BHHBF2_BRAIN_MALE", - "UCLA BHHBF2 Brain Male Only" - ], - [ - "UCLA_BHHBF2_BRAIN_FEMALE", - "UCLA BHHBF2 Brain Female Only" - ], - [ - "UCLA_BHHBF2_BRAIN_2005", - "UCLA BHHBF2 Brain (2005) mlratio **" - ] - ], - "Genotypes": [ - [ - "BHHBF2Geno", - "BHHBF2 Genotypes" - ] - ], - "Liver": [ - [ - "UCLA_BHHBF2_LIVER_MALE", - "UCLA BHHBF2 Liver Male Only" - ], - [ - "UCLA_BHHBF2_LIVER_FEMALE", - "UCLA BHHBF2 Liver Female Only" - ], - [ - "UCLA_BHHBF2_LIVER_2005", - "UCLA BHHBF2 Liver (2005) mlratio **" - ] - ], - "Muscle": [ - [ - "UCLA_BHHBF2_MUSCLE_MALE", - "UCLA BHHBF2 Muscle Male Only" - ], - [ - "UCLA_BHHBF2_MUSCLE_FEMALE", - "UCLA BHHBF2 Muscle Female Only" - ], - [ - "UCLA_BHHBF2_MUSCLE_2005", - "UCLA BHHBF2 Muscle (2005) mlratio **" - ] - ], - "Phenotypes": [ - [ - "BHHBF2Publish", - "BHHBF2 Published Phenotypes" - ] - ] - }, - "BXD": { - "Amygdala": [ - [ - "INIA_AmgCoh_0311", - "INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA" - ], - [ - "INIA_Amg_BLA_RMA_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA" - ], - [ - "INIA_Amg_BLA_RMA_M_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male" - ], - [ - "INIA_Amg_BLA_RMA_F_1110", - "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female" - ] - ], - "Brain": [ - [ - "BR_M2_1106_R", - "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" - ], - [ - "BR_U_1105_P", - "UTHSC Brain mRNA U74Av2 (Nov05) PDNN" - ], - [ - "BR_U_0805_M", - "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" - ], - [ - "BR_U_0805_R", - "UTHSC Brain mRNA U74Av2 (Aug05) RMA" - ], - [ - "BR_U_0805_P", - "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" - ], - [ - "CB_M_0204_P", - "INIA Brain mRNA M430 (Feb04) PDNN" - ] - ], - "Cartilage": [ - [ - "UCLA_BXDBXH_CARTILAGE_V2", - "UCLA BXD and BXH Cartilage v2" - ], - [ - "UCLA_BXDBXH_CARTILAGE", - "UCLA BXD and BXH Cartilage" - ], - [ - "UCLA_BXD_CARTILAGE", - "UCLA BXD Cartilage" - ] - ], - "Cerebellum": [ - [ - "CB_M_1004_M", - "SJUT Cerebellum mRNA M430 (Oct04) MAS5" - ], - [ - "CB_M_1004_R", - "SJUT Cerebellum mRNA M430 (Oct04) RMA" - ], - [ - "CB_M_1004_P", - "SJUT Cerebellum mRNA M430 (Oct04) PDNN" - ], - [ - "CB_M_1003_M", - "SJUT Cerebellum mRNA M430 (Oct03) MAS5" - ] - ], - "Eye": [ - [ - "Eye_M2_0908_R", - "Eye M430v2 (Sep08) RMA" - ], - [ - "Eye_M2_0908_R_NB", - "Eye M430v2 Mutant Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_ND", - "Eye M430v2 WT Gpnmb (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA **" - ], - [ - "Eye_M2_0908_WTWT", - "Eye M430v2 WT WT (Sep08) RMA **" - ], - [ - "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" - ], - [ - "BXD_GLA_0911", - "BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **" - ] - ], - "Genotypes": [ - [ - "BXDGeno", - "BXD Genotypes" - ] - ], - "Hematopoietic Cells": [ - [ - "UMCG_0907_HemaStem_ori", - "UMCG Stem Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_HemaStem", - "UMCG Stem Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "UMCG_0907_Pro_ori", - "UMCG Progenitor Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_Pro", - "UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "UMCG_0907_Eryth_ori", - "UMCG Erythroid Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_Eryth", - "UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "UMCG_0907_Myeloid_ori", - "UMCG Myeloid Cells ILM6v1.1 (Apr09) original" - ], - [ - "UMCG_0907_Myeloid", - "UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed" - ], - [ - "HC_U_0304_R", - "GNF Stem Cells U74Av2 (Mar04) RMA" - ] - ], - "Hippocampus": [ - [ - "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN" - ], - [ - "HC_M2_0606_M", - "Hippocampus Consortium M430v2 (Jun06) MAS5" - ], - [ - "HC_M2_0606_R", - "Hippocampus Consortium M430v2 (Jun06) RMA" - ], - [ - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ - "UT_ILM_BXD_hipp_NON_0909", - "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOS_0909", - "UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_NOE_0909", - "UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSS_0909", - "UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv" - ], - [ - "UT_ILM_BXD_hipp_RSE_0909", - "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" - ] - ], - "Hypothalamus": [ - [ - "INIA_Hyp_RMA_1110", - "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)" - ], - [ - "INIA_Hyp_M_RMA_1110", - "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Male" - ], - [ - "INIA_Hyp_F_RMA_1110", - "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female" - ] - ], - "Kidney": [ - [ - "MA_M2F_0706_R", - "Mouse kidney M430v2 Female (Aug06) RMA" - ], - [ - "MA_M2M_0706_R", - "Mouse kidney M430v2 Male (Aug06) RMA" - ], - [ - "MA_M2_0806_R", - "Mouse kidney M430v2 Sex Balanced (Aug06) RMA" - ], - [ - "MA_M2_0806_P", - "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" - ], - [ - "MA_M2_0706_P", - "Mouse Kidney M430v2 (Jul06) PDNN" - ], - [ - "MA_M2_0706_R", - "Mouse Kidney M430v2 (Jul06) RMA" - ] - ], - "Leucocytes": [ - [ - "Illum_BXD_PBL_1108", - "UWA Illumina PBL (Nov08) RSN **" - ] - ], - "Liver": [ - [ - "GSE16780_UCLA_ML0911", - "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" - ], - [ - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "SUH_Liv_RMA_0611", - "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" - ] - ], - "Lung": [ - [ - "HZI_0408_R", - "HZI Lung M430v2 (Apr08) RMA" - ], - [ - "HZI_0408_M", - "HZI Lung M430v2 (Apr08) MAS5" - ] - ], - "Midbrain": [ - [ - "VUBXDMouseMidBrainQ0212", - "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (Feb12) Quantile" - ] - ], - "Muscle": [ - [ - "EPFLMouseMuscleRMA1211", - "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleHFDRMA1211", - "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ], - [ - "EPFLMouseMuscleCDRMA1211", - "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" - ] - ], - "Neocortex": [ - [ - "DevNeocortex_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "DevNeocortex_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "HQFNeoc_1210v2_RankInv", - "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv" - ], - [ - "HQFNeoc_1210_RankInv", - "HQF BXD Neocortex ILM6v1.1 (Dec10) RankInv" - ], - [ - "HQFNeoc_0208_RankInv", - "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv" - ], - [ - "DevNeocortex_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv **" - ], - [ - "DevNeocortex_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv **" - ] - ], - "Nucleus Accumbens": [ - [ - "VCUSalo_1007_R", - "VCU BXD NA Sal M430 2.0 (Oct07) RMA" - ], - [ - "VCUEtOH_1007_R", - "VCU BXD NA EtOH M430 2.0 (Oct07) RMA **" - ], - [ - "VCUSal_1007_R", - "VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore **" - ] - ], - "Phenotypes": [ - [ - "BXDPublish", - "BXD Published Phenotypes" - ] - ], - "Prefrontal Cortex": [ - [ - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" - ], - [ - "VCUSal_1206_R", - "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" - ], - [ - "VCUSal_1006_R", - "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" - ], - [ - "VCU_PF_Air_0111_R", - "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_Et_0111_R", - "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **" - ], - [ - "VCU_PF_AvE_0111_Ss", - "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" - ] - ], - "Retina": [ - [ - "Illum_Retina_BXD_RankInv0410", - "HEI Retina Illumina V6.2 (April 2010) RankInv" - ], - [ - "B6D2ONCILM_0412", - "B6D2 ONC Illumina v6.1 (Apr12) RankInv **" - ], - [ - "ONCRetILM6_0412", - "ONC Retina Illumina V6.2 (Apr12) RankInv **" - ], - [ - "HEIONCvsCRetILM6_0911", - "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" - ], - [ - "G2HEIONCRetILM6_0911", - "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" - ], - [ - "HEIONCRetILM6_0911", - "HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" - ], - [ - "ILM_Retina_BXD_F_RankInv1210", - "HEI Retina Females Illumina V6.2 (Dec10) RankInv **" - ], - [ - "ILM_Retina_BXD_M_RankInv1210", - "HEI Retina Males Illumina V6.2 (Dec10) RankInv **" - ], - [ - "ILM_Retina_BXD_FM_RankInv1210", - "HEI Retina F-M Illumina V6.2 (Dec10) RankInv **" - ], - [ - "G2NEI_ILM_Retina_BXD_RI0410", - "G2NEI Retina Illumina V6.2 (April 2010) RankInv **" - ] - ], - "Spleen": [ - [ - "UTHSC_SPL_RMA_1210", - "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" - ], - [ - "UTHSC_SPL_RMA_1010", - "UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA" - ], - [ - "IoP_SPL_RMA_0509", - "IoP Affy MOE 430v2 Spleen (May09) RMA" - ], - [ - "Illum_BXD_Spl_1108", - "UWA Illumina Spleen (Nov08) RSN **" - ], - [ - "UTK_BXDSpl_VST_0110", - "UTK Spleen ILM6.1 (Jan10) VST" - ] - ], - "Striatum": [ - [ - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "UTHSC_Striatum_RankInv_1210", - "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" - ], - [ - "UTHSC_Str_RankInv_1210", - "HQF BXD Striatum ILM6.1 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"UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_FEMALE", - "UCLA CTB6B6CTF2 Brain Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" - ] - ], - "Genotypes": [ - [ - "CTB6F2Geno", - "CTB6F2 Genotypes" - ] - ], - "Liver": [ - [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" - ] - ], - "Muscle": [ - [ - "UCLA_CTB6B6CTF2_MUSCLE_MALE", - "UCLA CTB6B6CTF2 Muscle Male mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", - "UCLA CTB6B6CTF2 Muscle Female mlratio **" - ], - [ - "UCLA_CTB6B6CTF2_MUSCLE_2005", - "UCLA CTB6/B6CTF2 Muscle (2005) mlratio **" - ] - ], - "Phenotypes": [ - [ - "CTB6F2Publish", - "CTB6F2 Published Phenotypes" - ] - ] - }, - "CXB": { - "Genotypes": [ - [ - "CXBGeno", - "CXB Genotypes" - ] - ], - "Hippocampus": [ - [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ] - ], - "Phenotypes": [ - [ - "CXBPublish", - "CXB Published Phenotypes" - ] - ], - "Spleen": [ - [ - "STSPL_1107_R", - "Stuart Spleen M430v2 (Nov07) RMA" - ] - ] - }, - "HS": { - "Genotypes": [ - [ - "HSGeno", - "HS Genotypes" - ] - ], - "Hippocampus": [ - [ - "OXUKHS_ILMHipp_RI0510", - "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" - ] - ], - "Liver": [ - [ - "OXUKHS_ILMLiver_RI0510", - "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" - ] - ], - "Lung": [ - [ - "OXUKHS_ILMLung_RI0510", - "OX UK HS ILM6v1.1 Lung (May 2010) RankInv" - ] - ], - "Phenotypes": [ - [ - "HSPublish", - "HS Published Phenotypes" - ] - ] - }, - "HS-CC": { - "Genotypes": [ - [ - "HS-CCGeno", - "HS-CC Genotypes" - ] - ], - "Phenotypes": [ - [ - "HS-CCPublish", - "HS-CC Published Phenotypes" - ] - ], - "Striatum": [ - [ - "OHSU_HS-CC_ILMStr_0211", - "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" - ] - ] - }, - "LXS": { - "Genotypes": [ - [ - "LXSGeno", - "LXS Genotypes" - ] - ], - "Hippocampus": [ - [ - "Illum_LXS_Hipp_loess0807", - "Hippocampus Illumina (Aug07) LOESS" - ], - [ - "Illum_LXS_Hipp_loess_nb0807", - "Hippocampus Illumina (Aug07) LOESS_NB" - ], - [ - "Illum_LXS_Hipp_quant0807", - "Hippocampus Illumina (Aug07) QUANT" - ], - [ - "Illum_LXS_Hipp_quant_nb0807", - "Hippocampus Illumina (Aug07) QUANT_NB" - ], - [ - "Illum_LXS_Hipp_rsn0807", - "Hippocampus Illumina (Aug07) RSN" - ], - [ - "Illum_LXS_Hipp_rsn_nb0807", - "Hippocampus Illumina (Aug07) RSN_NB" - ], - [ - "Hipp_Illumina_RankInv_0507", - "Hippocampus Illumina (May07) RankInv" - ], - [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE 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"J12XJ58F2": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ] - ] - }, - "tomato": { - "LXP": [ - [ - "Phenotypes", - "Phenotypes" - ], - [ - "Genotypes", - "Genotypes" - ] - ] - } - } -} \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_items.js b/wqflask/wqflask/static/new/javascript/dataset_select_items.js deleted file mode 100755 index 33ff34cb..00000000 --- a/wqflask/wqflask/static/new/javascript/dataset_select_items.js +++ /dev/null @@ -1,773 +0,0 @@ -window.sArr = [ -{txt:'',val:''}, -{txt:'Human',val:'human'}, -{txt:'Macaque monkey',val:'macaque monkey'}, -{txt:'Mouse',val:'mouse'}, -{txt:'Rat',val:'rat'}, -{txt:'Drosophila',val:'drosophila'}, -{txt:'Arabidopsis thaliana',val:'arabidopsis'}, -{txt:'Barley',val:'barley'}, -{txt:'Soybean',val:'soybean'}, -{txt:'Tomato',val:'tomato'}, -{txt:'All Species',val:'All Species'}]; - -window.gArr = [ -{txt:'',val:''}, -{txt:'AD Cases & Controls 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-{txt:'J12XJ58F2',val:'J12XJ58F2'}, -{txt:'LXP',val:'LXP'}, -{txt:'LXS',val:'LXS'}, -{txt:'Macaca fasicularis (Cynomolgus monkey)',val:'Macaca-fasicularis'}, -{txt:'Mouse Diversity Panel',val:'MDP'}, -{txt:'NZB/FVB N2 NCI',val:'NZBXFVB-N2'}, -{txt:'Oregon-R x 2b3',val:'Oregon-R_x_2b3'}, -{txt:'QSM',val:'QSM'}, -{txt:'UIOWA SRxSHRSP F2',val:'SRxSHRSPF2'}, -{txt:'SXM',val:'SXM'}, -{txt:'All Groups',val:'all groups'}]; - -window.tArr = [ -{txt:'',val:''}, -{txt:'Adipose mRNA',val:'Adipose'}, -{txt:'Adrenal Gland mRNA',val:'Adrenal Gland'}, -{txt:'Amygdala mRNA',val:'Amygdala'}, -{txt:'Brain mRNA',val:'Brain'}, -{txt:'Cartilage mRNA',val:'Cartilage'}, -{txt:'Caudal Ganglionic Eminence mRNA',val:'Caudal Ganglionic Eminence'}, -{txt:'Cerebellar Cortex mRNA',val:'Cerebellar Cortex'}, -{txt:'Cerebellum mRNA',val:'Cerebellum'}, -{txt:'Diencephalon mRNA',val:'Diencephalon'}, -{txt:'Dorsal Thalamus mRNA',val:'Dorsal Thalamus'}, -{txt:'Dorsolateral Prefrontal Cortex mRNA',val:'Dorsolateral Prefrontal Cortex'}, -{txt:'Embryo mRNA',val:'Embryo'}, -{txt:'Eye mRNA',val:'Eye'}, -{txt:'Frontal Cerebral Wall mRNA',val:'Frontal Cerebral Wall'}, -{txt:'Heart mRNA',val:'Heart'}, -{txt:'Hematopoietic Cells mRNA',val:'Hematopoietic Cells'}, -{txt:'Hippocampus mRNA',val:'Hippocampus'}, -{txt:'Hypothalamus mRNA',val:'Hypothalamus'}, -{txt:'Inferior Temporal Cortex mRNA',val:'Inferior Temporal Cortex'}, -{txt:'Kidney mRNA',val:'Kidney'}, -{txt:'Lateral Ganglionic Eminence mRNA',val:'Lateral Ganglionic Eminence'}, -{txt:'Leaf mRNA',val:'Leaf'}, -{txt:'Leucocytes mRNA',val:'Leucocytes'}, -{txt:'Liver mRNA',val:'Liver'}, -{txt:'Lung mRNA',val:'Lung'}, -{txt:'Lymphoblast B-cell mRNA',val:'Lymphoblast B-cell'}, -{txt:'Mammary Tumors mRNA',val:'Mammary Tumors'}, -{txt:'Medial Ganglionic Eminence mRNA',val:'Medial Ganglionic Eminence'}, -{txt:'Medial Prefrontal Cortex mRNA',val:'Medial Prefrontal Cortex'}, -{txt:'Mediodorsal Nucleus of Thalamus mRNA',val:'Mediodorsal Nucleus of Thalamus'}, -{txt:'Midbrain mRNA',val:'Midbrain'}, -{txt:'Muscle mRNA',val:'Muscle'}, -{txt:'Neocortex mRNA',val:'Neocortex'}, -{txt:'Newborn Cord Blood mRNA',val:'Newborn Cord Blood'}, -{txt:'Nucleus Accumbens mRNA',val:'Nucleus Accumbens'}, -{txt:'Occipital Cerebral Wall mRNA',val:'Occipital Cerebral Wall'}, -{txt:'Orbital Prefrontal Cortex mRNA',val:'Orbital Prefrontal Cortex'}, -{txt:'Parietal Cerebral Wall mRNA',val:'Parietal Cerebral Wall'}, -{txt:'Peritoneal Fat mRNA',val:'Peritoneal Fat'}, -{txt:'Posterior Inferior Parietal Cortex mRNA',val:'Posterior Inferior Parietal Cortex'}, -{txt:'Posterior Superior Temporal Cortex mRNA',val:'Posterior Superior Temporal Cortex'}, -{txt:'Prefrontal Cortex mRNA',val:'Prefrontal Cortex'}, -{txt:'Primary Auditory (A1) Cortex mRNA',val:'Primary Auditory (A1) Cortex'}, -{txt:'Primary Motor (M1) Cortex mRNA',val:'Primary Motor (M1) Cortex'}, -{txt:'Primary Somatosensory (S1) Cortex mRNA',val:'Primary Somatosensory (S1) Cortex'}, -{txt:'Primary Visual Cortex mRNA',val:'Primary Visual Cortex'}, -{txt:'Retina mRNA',val:'Retina'}, -{txt:'Spleen mRNA',val:'Spleen'}, -{txt:'Striatum mRNA',val:'Striatum'}, -{txt:'T Cell (helper) mRNA',val:'T Cell (helper)'}, -{txt:'T Cell (regulatory) mRNA',val:'T Cell (regulatory)'}, -{txt:'Temporal Cerebral Wall mRNA',val:'Temporal Cerebral Wall'}, -{txt:'Thymus mRNA',val:'Thymus'}, -{txt:'Upper (Rostral) Rhombic Lip mRNA',val:'Upper (Rostral) Rhombic Lip'}, -{txt:'Ventral Forebrain mRNA',val:'Ventral Forebrain'}, -{txt:'Ventral Tegmental Area mRNA',val:'Ventral Tegmental Area'}, -{txt:'Ventrolateral Prefrontal Cortex mRNA',val:'Ventrolateral Prefrontal Cortex'}, -{txt:'Whole Body mRNA',val:'Whole Body'}, -{txt:'Phenotypes',val:'Phenotypes'}, -{txt:'Genotypes',val:'Genotypes'}]; - -window.dArr = [ -{txt:'',val:''}, -{txt:'GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv',val:'GSE15222_F_A_RI_0409'}, -{txt:'GSE15222 Human Brain Normal Myers (Apr09) RankInv',val:'GSE15222_F_N_RI_0409'}, -{txt:'Normal HEI Retina (April 2010) RankInv',val:'G2NEI_ILM_Retina_BXD_RI0410'}, -{txt:'Full HEI Retina (April 2010) RankInv',val:'Illum_Retina_BXD_RankInv0410'}, -{txt:'ONC HEI Retina (April 2012) RankInv',val:'ONCRetILM6_0412'}, -{txt:'B6D2 ONC Retina (April 2012) RankInv **',val:'B6D2ONCILM_0412'}, -{txt:'INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA **',val:'INIA_MacFas_Ac_RMA_0110'}, -{txt:'UCLA CTB6/B6CTF2 Liver (2005) mlratio',val:'UCLA_CTB6B6CTF2_LIVER_2005'}, -{txt:'UCLA CTB6/B6CTF2 Adipose (2005) mlratio',val:'UCLA_CTB6B6CTF2_ADIPOSE_2005'}, -{txt:'UCLA CTB6/B6CTF2 Brain (2005) mlratio',val:'UCLA_CTB6B6CTF2_BRAIN_2005'}, -{txt:'UCLA CTB6/B6CTF2 Muscle (2005) mlratio',val:'UCLA_CTB6B6CTF2_MUSCLE_2005'}, -{txt:'INIA Macaca fasicularis Hippocampus (Jan10) RMA **',val:'INIA_MacFas_Hc_RMA_0110'}, -{txt:'UCLA CTB6B6CTF2 Muscle Female mlratio **',val:'UCLA_CTB6B6CTF2_MUSCLE_FEMALE'}, -{txt:'INIA Macaca fasicularis Amygdala (Jan10) RMA **',val:'INIA_MacFas_AMG_RMA_0110'}, -{txt:'UCLA CTB6B6CTF2 Adipose Female mlratio **',val:'UCLA_CTB6B6CTF2_ADIPOSE_FEMALE'}, -{txt:'UCLA CTB6B6CTF2 Brain Female mlratio **',val:'UCLA_CTB6B6CTF2_BRAIN_FEMALE'}, -{txt:'UCLA CTB6B6CTF2 Liver Female mlratio **',val:'UCLA_CTB6B6CTF2_LIVER_FEMALE'}, -{txt:'VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **',val:'VUBXDMouseMidBrainQ0512'}, -{txt:'GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA',val:'GSE16780_UCLA_ML0911'}, -{txt:'EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **',val:'EPFLMouseMuscleRMA1211'}, -{txt:'EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **',val:'EPFLMouseMuscleHFDRMA1211'}, -{txt:'EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **',val:'EPFLMouseMuscleCDRMA1211'}, -{txt:'BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **',val:'DevStriatum_ILM6.2P14RInv_1111'}, -{txt:'BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **',val:'DevStriatum_ILM6.2P3RInv_1111'}, -{txt:'BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv',val:'DevNeocortex_ILM6.2P14RInv_1111'}, -{txt:'BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv',val:'DevNeocortex_ILM6.2P3RInv_1111'}, -{txt:'G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **',val:'G2HEIONCRetILM6_0911'}, -{txt:'HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **',val:'HEIONCvsCRetILM6_0911'}, -{txt:'JAX Liver Affy M430 2.0 (Jul11) MDP',val:'JAX_CSB_L_0711'}, -{txt:'JAX Liver HF Affy M430 2.0 (Jul11) MDP',val:'JAX_CSB_L_HF_0711'}, -{txt:'JAX Liver 6C Affy M430 2.0 (Jul11) MDP',val:'JAX_CSB_L_6C_0711'}, -{txt:'CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT **',val:'CANDLE_NB_0711'}, -{txt:'KIN/YSM Human AMY Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_AMY_0711'}, -{txt:'KIN/YSM Human A1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_A1C_0711'}, -{txt:'KIN/YSM Human TC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_TC_0711'}, -{txt:'KIN/YSM Human CBC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_CBC_0711'}, -{txt:'KIN/YSM Human CGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_CGE_0711'}, -{txt:'KIN/YSM Human FC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_FC_0711'}, -{txt:'KIN/YSM Human S1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_S1C_0711'}, -{txt:'KIN/YSM Human STR Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_STR_0711'}, -{txt:'KIN/YSM Human URL Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_URL_0711'}, -{txt:'KIN/YSM Human V1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_V1C_0711'}, -{txt:'KIN/YSM Human VF Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_VF_0711'}, -{txt:'KIN/YSM Human VFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_VFC_0711'}, -{txt:'KIN/YSM Human STC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_STC_0711'}, -{txt:'KIN/YSM Human ITC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_ITC_0711'}, -{txt:'KIN/YSM Human LGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_LGE_0711'}, -{txt:'KIN/YSM Human M1C Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_M1C_0711'}, -{txt:'KIN/YSM Human MD Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_MD_0711'}, -{txt:'KIN/YSM Human IPC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_IPC_0711'}, -{txt:'KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_HIP_0711'}, -{txt:'KIN/YSM Human MFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_MFC_0711'}, -{txt:'KIN/YSM Human DFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_DFC_0711'}, -{txt:'KIN/YSM Human DIE Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_DIE_0711'}, -{txt:'KIN/YSM Human MGE Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_MGE_0711'}, -{txt:'KIN/YSM Human DTH Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_DTH_0711'}, -{txt:'KIN/YSM Human PC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_PC_0711'}, -{txt:'KIN/YSM Human OC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_OC_0711'}, -{txt:'KIN/YSM Human OFC Affy Hu-Exon 1.0 ST (Jul11) Quantile **',val:'KIN_YSM_OFC_0711'}, -{txt:'HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio',val:'HBTRC-MLC_0611'}, -{txt:'HBTRC-MLC Human Cerebellum Agilent Normal (Jun11) mlratio',val:'HBTRC-MLC_N_0611'}, -{txt:'HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio',val:'HBTRC-MLPFC_0611'}, -{txt:'HBTRC-MLC Human Cerebellum Agilent AD (Jun11) mlratio',val:'HBTRC-MLC_AD_0611'}, -{txt:'HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio',val:'HBTRC-MLVC_0611'}, -{txt:'HBTRC-MLC Human Prefrontal Cortex Agilent Normal (Jun11) mlratio',val:'HBTRC-MLPFC_N_0611'}, -{txt:'HBTRC-MLC Human Prefrontal Cortex Agilent AD (Jun11) mlratio',val:'HBTRC-MLPFC_AD_0611'}, -{txt:'HBTRC-MLC Human Cerebellum Agilent HD (Jun11) mlratio',val:'HBTRC-MLC_HD_0611'}, -{txt:'HBTRC-MLC Human Visual Cortex Agilent Normal (Jun11) mlratio',val:'HBTRC-MLVC_N_0611'}, -{txt:'HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio',val:'HBTRC-MLPFC_HD_0611'}, -{txt:'HBTRC-MLC Human Visual Cortex Agilent AD (Jun11) mlratio',val:'HBTRC-MLVC_AD_0611'}, -{txt:'HBTRC-MLC Human Visual Cortex Agilent HD (Jun11) mlratio',val:'HBTRC-MLVC_HD_0611'}, -{txt:'INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA',val:'INIA_AmgCoh_0311'}, -{txt:'INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA',val:'INIA_Amg_BLA_RMA_1110'}, -{txt:'INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Male',val:'INIA_Amg_BLA_RMA_M_1110'}, -{txt:'INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female',val:'INIA_Amg_BLA_RMA_F_1110'}, -{txt:'GSE9588 Human Liver Normal (Mar11) Both Sexes',val:'HLC_0311'}, -{txt:'GSE9588 Human Liver Normal (Mar11) Males',val:'HLCM_0311'}, -{txt:'HZI Thelp M430v2 (Feb11) RMA',val:'RTHC_0211_R'}, -{txt:'GSE5281 Human Brain Normal Full Liang (Jul09) RMA',val:'GSE5281_F_RMA_N_0709'}, -{txt:'GSE5281 Human Brain Alzheimer Full Liang (Jul09) RMA',val:'GSE5281_F_RMA_Alzh_0709'}, -{txt:'OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv',val:'OHSU_HS-CC_ILMStr_0211'}, -{txt:'NCSU Drosophila Whole Body (Jan11) RMA',val:'NCSU_DrosWB_LC_RMA_0111'}, -{txt:'UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females',val:'LV_G_0106_F'}, -{txt:'UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males',val:'LV_G_0106_M'}, -{txt:'UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes',val:'LV_G_0106_B'}, -{txt:'GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **',val:'GenEx_BXD_liverSal_RMA_F_0211'}, -{txt:'GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **',val:'GenEx_BXD_liverSal_RMA_M_0211'}, -{txt:'GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **',val:'GenEx_BXD_liverSal_RMA_0211'}, -{txt:'GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **',val:'GenEx_BXD_liverEt_RMA_F_0211'}, -{txt:'GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **',val:'GenEx_BXD_liverEt_RMA_M_0211'}, -{txt:'GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **',val:'GenEx_BXD_liverEt_RMA_0211'}, -{txt:'SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **',val:'SUH_Liv_RMA_0611'}, -{txt:'HQF BXD Striatum ILM6.1 (Dec10v2) RankInv',val:'UTHSC_Striatum_RankInv_1210'}, -{txt:'HQF BXD Striatum ILM6.1 (Dec10) RankInv',val:'UTHSC_Str_RankInv_1210'}, -{txt:'HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv',val:'HQFNeoc_1210v2_RankInv'}, -{txt:'UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA',val:'UTHSC_SPL_RMA_1210'}, -{txt:'HQF BXD Neocortex ILM6v1.1 (Dec10) RankInv',val:'HQFNeoc_1210_RankInv'}, -{txt:'INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)',val:'INIA_Hyp_RMA_1110'}, -{txt:'INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Male',val:'INIA_Hyp_M_RMA_1110'}, -{txt:'INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female',val:'INIA_Hyp_F_RMA_1110'}, -{txt:'UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA',val:'UTHSC_SPL_RMA_1010'}, -{txt:'Hippocampus Consortium M430v2 (Jun06) RMA MDP',val:'HC_M2_0606_MDP'}, -{txt:'UMUTAffy Hippocampus Exon (Feb09) RMA MDP',val:'UMUTAffyExon_0209_RMA_MDP'}, -{txt:'OX UK HS ILM6v1.1 Lung (May 2010) RankInv',val:'OXUKHS_ILMLung_RI0510'}, -{txt:'OX UK HS ILM6v1.1 Liver (May 2010) RankInv',val:'OXUKHS_ILMLiver_RI0510'}, -{txt:'OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv',val:'OXUKHS_ILMHipp_RI0510'}, -{txt:'INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA **',val:'INIA_MacFas_Pf_RMA_0110'}, -{txt:'INIA Macaca fasicularis Brain (Jan10) RMA **',val:'INIA_MacFas_brain_RMA_0110'}, -{txt:'UAB Whole body D.m. mRNA control (Oct09) RMA',val:'UAB_DrosWB_LC_RMA_1009'}, -{txt:'UAB Whole body D.m. mRNA lead (pbAc) (Oct09) RMA',val:'UAB_DrosWB_LE_RMA_1009'}, -{txt:'UMCG Stem Cells ILM6v1.1 (Apr09) original',val:'UMCG_0907_HemaStem_ori'}, -{txt:'UMCG Stem Cells ILM6v1.1 (Apr09) transformed',val:'UMCG_0907_HemaStem'}, -{txt:'UMCG Progenitor Cells ILM6v1.1 (Apr09) original',val:'UMCG_0907_Pro_ori'}, -{txt:'UMCG Progenitor Cells ILM6v1.1 (Apr09) transformed',val:'UMCG_0907_Pro'}, -{txt:'UMCG Erythroid Cells ILM6v1.1 (Apr09) original',val:'UMCG_0907_Eryth_ori'}, -{txt:'UMCG Erythroid Cells ILM6v1.1 (Apr09) transformed',val:'UMCG_0907_Eryth'}, -{txt:'UMCG Myeloid Cells ILM6v1.1 (Apr09) original',val:'UMCG_0907_Myeloid_ori'}, -{txt:'UMCG Myeloid Cells ILM6v1.1 (Apr09) transformed',val:'UMCG_0907_Myeloid'}, -{txt:'UTHSC CEPH B-cells Illumina (Sep09) RankInv',val:'UT_CEPH_RankInv0909'}, -{txt:'Mouse kidney M430v2 Female (Aug06) RMA',val:'MA_M2F_0706_R'}, -{txt:'Mouse kidney M430v2 Male (Aug06) RMA',val:'MA_M2M_0706_R'}, -{txt:'Barley1 Leaf INOC TTKS (Aug09) RMA',val:'B1LI0809R'}, -{txt:'Barley1 Leaf INOC TTKS (Aug09) MAS5',val:'B1LI0809M5'}, -{txt:'Barley1 Leaf MOCK TTKS (Aug09) MAS5',val:'B1MI0809M5'}, -{txt:'Barley1 Leaf MOCK TTKS (Aug09) RMA',val:'B1MI0809R'}, -{txt:'GSE15222 Human Brain Myers (Apr09) RankInv',val:'GSE15222_F_RI_0409'}, -{txt:'GSE5281 Human Brain Full Liang (Jul09) RMA',val:'GSE5281_F_RMA0709'}, -{txt:'GSE5281 Human Brain Best 102 Liang (Jul09) RMA',val:'GSE5281_RMA0709'}, -{txt:'UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA',val:'UT_HippRatEx_RMA_0709'}, -{txt:'VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **',val:'VCUEtOH_0609_R'}, -{txt:'VCU BXD VTA Sal M430 2.0 (Jun09) RMA **',val:'VCUSal_0609_R'}, -{txt:'VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **',val:'VCUEtvsSal_0609_R'}, -{txt:'IoP Affy MOE 430v2 Spleen (May09) RMA',val:'IoP_SPL_RMA_0509'}, -{txt:'NCI Mammary M430v2 (Apr09) RMA',val:'NCI_Mam_Tum_RMA_0409'}, -{txt:'NCI Mammary LMT miRNA v2 (Apr09) RMA',val:'NCI_Agil_Mam_Tum_RMA_0409'}, -{txt:'MDC/CAS/UCL Liver 230v2 (Dec08) RMA',val:'HXB_Liver_1208'}, -{txt:'MDC/CAS/UCL Heart 230_V2 (Dec08) RMA',val:'HXB_Heart_1208'}, -{txt:'MDC/CAS/UCL Adrenal 230A (Dec08) RMA',val:'HXB_Adrenal_1208'}, -{txt:'UWA Illumina PBL (Nov08) RSN **',val:'Illum_BXD_PBL_1108'}, -{txt:'UWA Illumina Thymus (Nov08) RSN **',val:'Illum_BXD_Thy_1108'}, -{txt:'UWA Illumina Spleen (Nov08) RSN **',val:'Illum_BXD_Spl_1108'}, -{txt:'Monks CEPH B-cells Agilent (Dec04) Log10Ratio',val:'Human_1008'}, -{txt:'UTK Spleen ILM6.1 (Jan10) VST',val:'UTK_BXDSpl_VST_0110'}, -{txt:'Eye AXBXA Illumina V6.2(Oct08) RankInv Beta',val:'Eye_AXBXA_1008_RankInv'}, -{txt:'Eye M430v2 (Sep08) RMA',val:'Eye_M2_0908_R'}, -{txt:'Eye M430v2 Mutant Gpnmb (Sep08) RMA **',val:'Eye_M2_0908_R_NB'}, -{txt:'Eye M430v2 WT Gpnmb (Sep08) RMA **',val:'Eye_M2_0908_R_ND'}, -{txt:'Eye M430v2 Mutant Tyrp1 (Sep08) RMA **',val:'Eye_M2_0908_R_MT'}, -{txt:'Eye M430v2 WT WT (Sep08) RMA **',val:'Eye_M2_0908_WTWT'}, -{txt:'Eye M430v2 WT Tyrp1 (Sep08) RMA **',val:'Eye_M2_0908_R_WT'}, -{txt:'BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **',val:'BXD_GLA_0911'}, -{txt:'UCLA BXH and BXD Cartilage v2',val:'UCLA_BXHBXD_CARTILAGE_V2'}, -{txt:'UCLA BXD and BXH Cartilage v2',val:'UCLA_BXDBXH_CARTILAGE_V2'}, -{txt:'UCLA BXD and BXH Cartilage',val:'UCLA_BXDBXH_CARTILAGE'}, -{txt:'UCLA BXH and BXD Cartilage',val:'UCLA_BXHBXD_CARTILAGE'}, -{txt:'UCLA BHF2 Brain Male mlratio',val:'UCLA_BHF2_BRAIN_MALE'}, -{txt:'UCLA BHF2 Brain Female mlratio',val:'UCLA_BHF2_BRAIN_FEMALE'}, -{txt:'UCLA BHF2 Adipose Female mlratio',val:'UCLA_BHF2_ADIPOSE_FEMALE'}, -{txt:'UCLA BHF2 Adipose Male mlratio',val:'UCLA_BHF2_ADIPOSE_MALE'}, -{txt:'UCLA CTB6B6CTF2 Muscle Male mlratio **',val:'UCLA_CTB6B6CTF2_MUSCLE_MALE'}, -{txt:'UCLA CTB6B6CTF2 Liver Male mlratio **',val:'UCLA_CTB6B6CTF2_LIVER_MALE'}, -{txt:'UCLA CTB6B6CTF2 Brain Male mlratio **',val:'UCLA_CTB6B6CTF2_BRAIN_MALE'}, -{txt:'UCLA CTB6B6CTF2 Adipose Male mlratio **',val:'UCLA_CTB6B6CTF2_ADIPOSE_MALE'}, -{txt:'UCLA BHF2 Liver Male mlratio',val:'UCLA_BHF2_LIVER_MALE'}, -{txt:'UCLA BHF2 Liver Female mlratio',val:'UCLA_BHF2_LIVER_FEMALE'}, -{txt:'UCLA BHHBF2 Brain Female Only',val:'UCLA_BHHBF2_BRAIN_FEMALE'}, -{txt:'UCLA BHHBF2 Liver Female Only',val:'UCLA_BHHBF2_LIVER_FEMALE'}, -{txt:'UCLA BHHBF2 Muscle Male Only',val:'UCLA_BHHBF2_MUSCLE_MALE'}, -{txt:'UCLA BHHBF2 Muscle Female Only',val:'UCLA_BHHBF2_MUSCLE_FEMALE'}, -{txt:'UCLA BHHBF2 Liver Male Only',val:'UCLA_BHHBF2_LIVER_MALE'}, -{txt:'UCLA BHHBF2 Brain Male Only',val:'UCLA_BHHBF2_BRAIN_MALE'}, -{txt:'UCLA BHHBF2 Adipose Female Only',val:'UCLA_BHHBF2_ADIPOSE_FEMALE'}, -{txt:'UCLA BHHBF2 Adipose Male Only',val:'UCLA_BHHBF2_ADIPOSE_MALE'}, -{txt:'UCLA BHF2 Muscle Female mlratio **',val:'UCLA_BHF2_MUSCLE_FEMALE'}, -{txt:'UCLA BHF2 Muscle Male mlratio **',val:'UCLA_BHF2_MUSCLE_MALE'}, -{txt:'UCLA BXH Cartilage',val:'UCLA_BXH_CARTILAGE'}, -{txt:'UCLA BXD Cartilage',val:'UCLA_BXD_CARTILAGE'}, -{txt:'UCLA BHHBF2 Adipose (2005) mlratio **',val:'UCLA_BHHBF2_ADIPOSE_2005'}, -{txt:'UCLA BHHBF2 Brain (2005) mlratio **',val:'UCLA_BHHBF2_BRAIN_2005'}, -{txt:'UCLA BHHBF2 Liver (2005) mlratio **',val:'UCLA_BHHBF2_LIVER_2005'}, -{txt:'UCLA BHHBF2 Muscle (2005) mlratio **',val:'UCLA_BHHBF2_MUSCLE_2005'}, -{txt:'UCLA BHF2 Adipose (June05) mlratio',val:'UCLA_BHF2_ADIPOSE_0605'}, -{txt:'UCLA BDF2 Liver (1999) mlratio',val:'UCLA_BDF2_LIVER_1999'}, -{txt:'UCLA BHF2 Muscle (June05) mlratio **',val:'UCLA_BHF2_MUSCLE_0605'}, -{txt:'UCLA BHF2 Brain (June05) mlratio',val:'UCLA_BHF2_BRAIN_0605'}, -{txt:'UCLA BHF2 Liver (June05) mlratio',val:'UCLA_BHF2_LIVER_0605'}, -{txt:'HZI Lung M430v2 (Apr08) RMA',val:'HZI_0408_R'}, -{txt:'HZI Lung M430v2 (Apr08) MAS5',val:'HZI_0408_M'}, -{txt:'HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv',val:'HQFNeoc_0208_RankInv'}, -{txt:'VCU BXD NA Sal M430 2.0 (Oct07) RMA',val:'VCUSalo_1007_R'}, -{txt:'VCU BXD NA EtOH M430 2.0 (Oct07) RMA **',val:'VCUEtOH_1007_R'}, -{txt:'VCU BXD NA Et vs Sal M430 2.0 (Oct07) Sscore **',val:'VCUSal_1007_R'}, -{txt:'Stuart Spleen M430v2 (Nov07) RMA',val:'STSPL_1107_R'}, -{txt:'HQF BXD Striatum ILM6.1 (Nov07) RankInv',val:'UTHSC_1107_RankInv'}, -{txt:'Hippocampus Illumina (Aug07) LOESS',val:'Illum_LXS_Hipp_loess0807'}, -{txt:'Hippocampus Illumina (Aug07) LOESS_NB',val:'Illum_LXS_Hipp_loess_nb0807'}, -{txt:'Hippocampus Illumina (Aug07) QUANT',val:'Illum_LXS_Hipp_quant0807'}, -{txt:'Hippocampus Illumina (Aug07) QUANT_NB',val:'Illum_LXS_Hipp_quant_nb0807'}, -{txt:'Hippocampus Illumina (Aug07) RSN',val:'Illum_LXS_Hipp_rsn0807'}, -{txt:'Hippocampus Illumina (Aug07) RSN_NB',val:'Illum_LXS_Hipp_rsn_nb0807'}, -{txt:'VCU BXD PFC EtOH M430 2.0 (Dec06) RMA',val:'VCUEtOH_1206_R'}, -{txt:'VCU BXD PFC Sal M430 2.0 (Dec06) RMA',val:'VCUSal_1206_R'}, -{txt:'VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore',val:'VCUSal_1006_R'}, -{txt:'VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **',val:'VCU_PF_Air_0111_R'}, -{txt:'VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **',val:'VCU_PF_Et_0111_R'}, -{txt:'VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **',val:'VCU_PF_AvE_0111_Ss'}, -{txt:'Hippocampus Illumina (May07) RankInv',val:'Hipp_Illumina_RankInv_0507'}, -{txt:'VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **',val:'VCUEtOH_0806_R'}, -{txt:'VCU LXS PFC Sal M430A 2.0 (Aug06) RMA',val:'VCUSal_0806_R'}, -{txt:'VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **',val:'VCUEt_vs_Sal_0806_R'}, -{txt:'Barley1 Embryo gcRMA SCRI (Dec06)',val:'B139_K_1206_R'}, -{txt:'Barley1 Leaf MAS 5.0 SCRI (Dec06)',val:'B30_K_1206_M'}, -{txt:'Barley1 Leaf gcRMAn SCRI (Dec06)',val:'B30_K_1206_Rn'}, -{txt:'Barley1 Leaf gcRMA SCRI (Dec06)',val:'B30_K_1206_R'}, -{txt:'Barley1 Embryo MAS 5.0 SCRI (Dec06)',val:'B139_K_1206_M'}, -{txt:'UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA',val:'BR_M2_1106_R'}, -{txt:'HZI Treg M430v2 (Feb11) RMA',val:'RTC_1106_R'}, -{txt:'UIOWA Eye mRNA RAE230v2 (Sep06) RMA',val:'UIOWA_Eye_RMA_0906'}, -{txt:'Mouse kidney M430v2 Sex Balanced (Aug06) RMA',val:'MA_M2_0806_R'}, -{txt:'Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN',val:'MA_M2_0806_P'}, -{txt:'Mouse Kidney M430v2 (Jul06) PDNN',val:'MA_M2_0706_P'}, -{txt:'Mouse Kidney M430v2 (Jul06) RMA',val:'MA_M2_0706_R'}, -{txt:'Barley1 Embryo0 gcRMA SCRI (Apr06)',val:'B150_K_0406_R'}, -{txt:'INIA Brain mRNA M430 (Jun06) RMA',val:'IBR_M_0606_R'}, -{txt:'Hippocampus Consortium M430v2 (Jun06) PDNN',val:'HC_M2_0606_P'}, -{txt:'Hippocampus Consortium M430v2 (Jun06) MAS5',val:'HC_M2_0606_M'}, -{txt:'Hippocampus Consortium M430v2 (Jun06) RMA',val:'HC_M2_0606_R'}, -{txt:'INIA Brain mRNA M430 (Jan06) RMA',val:'IBR_M_0106_R'}, -{txt:'INIA Brain mRNA M430 (Jan06) PDNN',val:'IBR_M_0106_P'}, -{txt:'Hippocampus Consortium M430v2 CXB (Dec05) RMA',val:'HC_M2CB_1205_R'}, -{txt:'Hippocampus Consortium M430v2 CXB (Dec05) PDNN',val:'HC_M2CB_1205_P'}, -{txt:'UTHSC Brain mRNA U74Av2 (Nov05) PDNN',val:'BR_U_1105_P'}, -{txt:'UMUTAffy Hippocampus Exon (Feb09) RMA',val:'UMUTAffyExon_0209_RMA'}, -{txt:'UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv',val:'UT_ILM_BXD_hipp_NON_0909'}, -{txt:'UTHSC Hippocampus Illumina v6.1 NOS (Sep09) RankInv',val:'UT_ILM_BXD_hipp_NOS_0909'}, -{txt:'UTHSC Hippocampus Illumina v6.1 NOE (Sep09) RankInv',val:'UT_ILM_BXD_hipp_NOE_0909'}, -{txt:'UTHSC Hippocampus Illumina v6.1 RSS (Sep09) RankInv',val:'UT_ILM_BXD_hipp_RSS_0909'}, -{txt:'UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv',val:'UT_ILM_BXD_hipp_RSE_0909'}, -{txt:'OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN',val:'SA_M2_0905_P'}, -{txt:'OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA',val:'SA_M2_0905_R'}, -{txt:'OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5',val:'SA_M2_0905_M'}, -{txt:'UTHSC Brain mRNA U74Av2 (Aug05) RMA',val:'BR_U_0805_R'}, -{txt:'UTHSC Brain mRNA U74Av2 (Aug05) PDNN',val:'BR_U_0805_P'}, -{txt:'UTHSC Brain mRNA U74Av2 (Aug05) MAS5',val:'BR_U_0805_M'}, -{txt:'MDC/CAS/ICL Peritoneal Fat 230A (Aug05) MAS5',val:'FT_2A_0805_M'}, -{txt:'OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA',val:'BRF2_M_0805_R'}, -{txt:'OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN',val:'BRF2_M_0805_P'}, -{txt:'OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5',val:'BRF2_M_0805_M'}, -{txt:'MDC/CAS/ICL Peritoneal Fat 230A (Jun05) RMA 2z+8',val:'FT_2A_0605_Rz'}, -{txt:'HBP Rosen Striatum M430V2 (Apr05) MAS5 Clean',val:'SA_M2_0405_MC'}, -{txt:'GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN',val:'GCB_M2_0505_P'}, -{txt:'GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA',val:'GCB_M2_0505_R'}, -{txt:'GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5',val:'GCB_M2_0505_M'}, -{txt:'MDC/CAS/ICL Kidney 230A (Apr05) MAS5',val:'KI_2A_0405_M'}, -{txt:'HBP Rosen Striatum M430V2 (Apr05) RMA Clean',val:'SA_M2_0405_RC'}, -{txt:'HBP Rosen Striatum M430V2 (Apr05) PDNN Clean',val:'SA_M2_0405_PC'}, -{txt:'HBP Rosen Striatum M430V2 (Apr05) SScore',val:'SA_M2_0405_SS'}, -{txt:'HBP Rosen Striatum M430V2 (Apr05) RMA Orig',val:'SA_M2_0405_RR'}, -{txt:'MDC/CAS/ICL Kidney 230A (Apr05) RMA 2z+8',val:'KI_2A_0405_Rz'}, -{txt:'MDC/CAS/ICL Kidney 230A (Apr05) RMA',val:'KI_2A_0405_R'}, -{txt:'SJUT Cerebellum mRNA M430 (Mar05) PDNN',val:'CB_M_0305_P'}, -{txt:'SJUT Cerebellum mRNA M430 (Mar05) MAS5',val:'CB_M_0305_M'}, -{txt:'SJUT Cerebellum mRNA M430 (Mar05) RMA',val:'CB_M_0305_R'}, -{txt:'HQF Striatum Exon (Feb09) RMA',val:'Striatum_Exon_0209'}, -{txt:'BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv',val:'DevNeocortex_ILM6.2P14RInv_1110'}, -{txt:'BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **',val:'DevStriatum_ILM6.2P14RInv_1110'}, -{txt:'BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **',val:'DevStriatum_ILM6.2P3RInv_1110'}, -{txt:'BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv',val:'DevNeocortex_ILM6.2P3RInv_1110'}, -{txt:'SJUT Cerebellum mRNA M430 (Oct04) MAS5',val:'CB_M_1004_M'}, -{txt:'SJUT Cerebellum mRNA M430 (Oct04) PDNN',val:'CB_M_1004_P'}, -{txt:'SJUT Cerebellum mRNA M430 (Oct04) RMA',val:'CB_M_1004_R'}, -{txt:'(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5',val:'LVF2_M_0704_M'}, -{txt:'(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA',val:'LVF2_M_0704_R'}, -{txt:'NCI Mammary mRNA M430 (July04) MAS5',val:'MA_M_0704_M'}, -{txt:'NCI Mammary mRNA M430 (July04) RMA',val:'MA_M_0704_R'}, -{txt:'OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN',val:'BRF2_M_0304_P'}, -{txt:'OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA',val:'BRF2_M_0304_R'}, -{txt:'OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5',val:'BRF2_M_0304_M'}, -{txt:'GNF Stem Cells U74Av2 (Mar04) RMA',val:'HC_U_0304_R'}, -{txt:'INIA Brain mRNA M430 (Feb04) PDNN',val:'CB_M_0204_P'}, -{txt:'SJUT Cerebellum mRNA M430 (Oct03) MAS5',val:'CB_M_1003_M'}, -{txt:'Hippocampus Illumina NOS (Oct08) RankInv beta',val:'Illum_LXS_Hipp_NOS_1008'}, -{txt:'Hippocampus Illumina RSE (Oct08) RankInv beta',val:'Illum_LXS_Hipp_RSE_1008'}, -{txt:'GSE9588 Human Liver Normal (Mar11) Females',val:'HLCF_0311'}, -{txt:'Hippocampus Illumina RSS (Oct08) RankInv beta',val:'Illum_LXS_Hipp_RSS_1008'}, -{txt:'Hippocampus Illumina NOE (Oct08) RankInv beta',val:'Illum_LXS_Hipp_NOE_1008'}, -{txt:'Hippocampus Illumina NON (Oct08) RankInv beta',val:'Illum_LXS_Hipp_NON_1008'}, -{txt:'CANDLE Published Phenotypes',val:'CANDLEPublish'}, -{txt:'HLC Published Phenotypes',val:'HLCPublish'}, -{txt:'AKXD Genotypes',val:'AKXDGeno'}, -{txt:'AXBXA Published Phenotypes',val:'AXBXAPublish'}, -{txt:'AXBXA Genotypes',val:'AXBXAGeno'}, -{txt:'B6BTBRF2 Published Phenotypes',val:'B6BTBRF2Publish'}, -{txt:'B6BTBRF2 Genotypes',val:'B6BTBRF2Geno'}, -{txt:'B6D2F2 Genotypes',val:'B6D2F2Geno'}, -{txt:'BDF2-1999 Genotypes',val:'BDF2-1999Geno'}, -{txt:'BDF2-2005 Genotypes',val:'BDF2-2005Geno'}, -{txt:'BHF2 Genotypes',val:'BHF2Geno'}, -{txt:'BHHBF2 Genotypes',val:'BHHBF2Geno'}, -{txt:'BXD Published Phenotypes',val:'BXDPublish'}, -{txt:'BXD Genotypes',val:'BXDGeno'}, -{txt:'BXH Published Phenotypes',val:'BXHPublish'}, -{txt:'BXH Genotypes',val:'BXHGeno'}, -{txt:'CTB6F2 Published Phenotypes',val:'CTB6F2Publish'}, -{txt:'CTB6F2 Genotypes',val:'CTB6F2Geno'}, -{txt:'CXB Published Phenotypes',val:'CXBPublish'}, -{txt:'CXB Genotypes',val:'CXBGeno'}, -{txt:'LXS Published Phenotypes',val:'LXSPublish'}, -{txt:'LXS Genotypes',val:'LXSGeno'}, -{txt:'Mouse Phenome Database',val:'MDPPublish'}, -{txt:'MDP Genotypes',val:'MDPGeno'}, -{txt:'NZBXFVB-N2 Published Phenotypes',val:'NZBXFVB-N2Publish'}, -{txt:'HXBBXH Published Phenotypes',val:'HXBBXHPublish'}, -{txt:'HXBBXH Genotypes',val:'HXBBXHGeno'}, -{txt:'BayXSha Published Phenotypes',val:'BayXShaPublish'}, -{txt:'BayXSha Genotypes',val:'BayXShaGeno'}, -{txt:'ColXBur Published Phenotypes',val:'ColXBurPublish'}, -{txt:'ColXBur Genotypes',val:'ColXBurGeno'}, -{txt:'ColXCvi Published Phenotypes',val:'ColXCviPublish'}, -{txt:'ColXCvi Genotypes',val:'ColXCviGeno'}, -{txt:'SXM Published Phenotypes',val:'SXMPublish'}, -{txt:'SXM Genotypes',val:'SXMGeno'}, -{txt:'J12XJ58F2 Published Phenotypes',val:'J12XJ58F2Publish'}, -{txt:'LXP Published Phenotypes',val:'LXPPublish'}, -{txt:'All Phenotypes',val:'_allPublish'}]; - -window.lArr = [ - null, -[1,1,4,79], -[1,1,4,80], -[1,1,4,127], -[1,1,4,128], -[1,2,4,1], -[1,2,4,2], -[1,2,4,126], -[1,14,59,288], -[1,14,34,32], -[1,15,26,119], -[1,15,26,142], -[1,21,8,60], -[1,21,8,61], -[1,21,8,63], -[1,21,8,67], -[1,21,42,62], -[1,21,42,65], -[1,21,42,66], -[1,21,42,69], -[1,21,46,64], -[1,21,46,68], -[1,21,46,70], -[1,21,46,71], -[1,22,59,289], -[1,22,24,76], -[1,22,24,77], -[1,22,24,284], -[1,25,3,33], -[1,25,6,37], -[1,25,7,36], -[1,25,9,54], -[1,25,10,56], 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-[3,11,1,173], -[3,11,1,178], -[3,11,4,166], -[3,11,4,171], -[3,11,4,179], -[3,11,24,167], -[3,11,24,170], -[3,11,24,180], -[3,11,32,168], -[3,11,32,169], -[3,11,32,181], -[3,12,59,300], -[3,12,60,301], -[3,12,3,72], -[3,12,3,73], -[3,12,3,74], -[3,12,3,75], -[3,12,4,216], -[3,12,4,224], -[3,12,4,228], -[3,12,4,229], -[3,12,4,232], -[3,12,4,242], -[3,12,4,243], -[3,12,4,244], -[3,12,4,280], -[3,12,5,153], -[3,12,5,154], -[3,12,5,177], -[3,12,8,251], -[3,12,8,252], -[3,12,8,253], -[3,12,8,261], -[3,12,8,262], -[3,12,8,263], -[3,12,8,269], -[3,12,8,270], -[3,12,8,271], -[3,12,8,281], -[3,12,13,145], -[3,12,13,146], -[3,12,13,147], -[3,12,13,148], -[3,12,13,149], -[3,12,13,150], -[3,12,13,151], -[3,12,16,111], -[3,12,16,112], -[3,12,16,113], -[3,12,16,114], -[3,12,16,115], -[3,12,16,116], -[3,12,16,117], -[3,12,16,118], -[3,12,16,279], -[3,12,17,225], -[3,12,17,226], -[3,12,17,227], -[3,12,17,233], -[3,12,17,234], -[3,12,17,235], -[3,12,17,236], -[3,12,17,237], -[3,12,17,238], -[3,12,18,98], -[3,12,18,99], -[3,12,18,100], -[3,12,20,120], -[3,12,20,121], -[3,12,20,219], -[3,12,20,220], -[3,12,20,221], -[3,12,20,222], -[3,12,23,139], -[3,12,24,19], -[3,12,24,83], -[3,12,24,84], -[3,12,24,85], -[3,12,24,86], -[3,12,24,87], -[3,12,24,88], -[3,12,24,89], -[3,12,24,90], -[3,12,24,91], -[3,12,24,92], -[3,12,25,187], -[3,12,25,188], -[3,12,31,18], -[3,12,32,20], -[3,12,32,21], -[3,12,32,22], -[3,12,33,25], -[3,12,33,26], -[3,12,33,95], -[3,12,33,97], -[3,12,33,189], -[3,12,33,265], -[3,12,33,268], -[3,12,35,190], -[3,12,35,191], -[3,12,35,192], -[3,12,42,201], -[3,12,42,202], -[3,12,42,203], -[3,12,42,204], -[3,12,42,205], -[3,12,42,206], -[3,12,47,3], -[3,12,47,4], -[3,12,47,5], -[3,12,47,6], -[3,12,47,27], -[3,12,47,28], -[3,12,48,96], -[3,12,48,101], -[3,12,48,133], -[3,12,48,141], -[3,12,48,143], -[3,12,49,23], -[3,12,49,24], -[3,12,49,93], -[3,12,49,94], -[3,12,49,194], -[3,12,49,250], -[3,12,49,255], -[3,12,49,256], -[3,12,49,257], -[3,12,49,258], -[3,12,49,264], -[3,12,49,266], -[3,12,49,267], -[3,12,50,78], -[3,12,51,217], -[3,12,53,140], -[3,12,56,130], -[3,12,56,131], -[3,12,56,132], -[3,13,59,302], -[3,13,60,303], -[3,13,5,152], -[3,13,5,155], -[3,13,5,176], -[3,18,59,304], -[3,18,60,305], -[3,18,1,9], -[3,18,1,15], -[3,18,1,163], -[3,18,4,10], -[3,18,4,16], -[3,18,4,162], -[3,18,24,8], -[3,18,24,17], -[3,18,24,161], -[3,18,32,11], -[3,18,32,13], -[3,18,32,160], -[3,19,59,306], -[3,19,60,307], -[3,19,17,230], -[3,19,17,231], -[3,19,48,193], -[3,23,17,106], -[3,23,24,105], -[3,23,25,104], -[3,24,49,81], -[3,29,59,308], -[3,29,60,309], -[3,29,17,195], -[3,29,17,196], -[3,29,17,197], -[3,29,17,198], -[3,29,17,199], -[3,29,17,200], -[3,29,17,207], -[3,29,17,282], -[3,29,17,283], -[3,29,17,285], -[3,29,17,286], -[3,29,17,287], -[3,29,42,208], -[3,29,42,209], -[3,29,42,210], -[3,31,59,310], -[3,31,60,311], -[3,31,17,102], -[3,31,17,103], -[3,31,24,29], -[3,31,24,30], -[3,31,24,31], -[3,32,59,312], -[3,32,27,134], -[4,26,59,313], -[4,26,60,314], -[4,26,2,138], -[4,26,15,137], -[4,26,17,129], -[4,26,20,254], -[4,26,20,259], -[4,26,20,260], -[4,26,24,136], -[4,26,39,245], -[4,26,39,249], -[4,35,13,218], -[5,20,58,82], -[5,33,58,109], -[5,33,58,110], -[6,7,59,315], -[6,7,60,316], -[6,16,59,317], -[6,16,60,318], -[6,17,59,319], -[6,17,60,320], -[7,34,22,122], -[7,34,22,123], -[7,34,22,124], -[7,34,22,125], -[7,36,59,321], -[7,36,60,322], -[7,36,12,211], -[7,36,12,215], -[7,36,12,223], -[7,36,22,212], -[7,36,22,213], -[7,36,22,214], -[8,27,59,323], -[9,28,59,324], -[10,37,59,325]]; - - diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee index df891826..a58efe2e 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee @@ -7,7 +7,7 @@ $ -> populate_species() apply_default() - $.ajax '/static/new/javascript/dataset_menu_structure', + $.ajax '/static/new/javascript/dataset_menu_structure.json', dataType: 'json' success: process_json @@ -15,6 +15,7 @@ $ -> species_list = @jdata.species redo_dropdown($('#species'), species_list) populate_group() + window.populate_species = populate_species populate_group = -> console.log("in populate group") @@ -22,6 +23,7 @@ $ -> group_list = @jdata.groups[species] redo_dropdown($('#group'), group_list) populate_type() + window.populate_group = populate_group populate_type = -> species = $('#species').val() @@ -29,6 +31,7 @@ $ -> type_list = @jdata.types[species][group] redo_dropdown($('#type'), type_list) populate_dataset() + window.populate_type = populate_type populate_dataset = -> species = $('#species').val() @@ -38,6 +41,7 @@ $ -> dataset_list = @jdata.datasets[species][group][type] console.log("pop_dataset:", dataset_list) redo_dropdown($('#dataset'), dataset_list) + window.populate_dataset = populate_dataset redo_dropdown = (dropdown, items) -> console.log("in redo:", dropdown, items) @@ -99,7 +103,9 @@ $ -> $("##{item[0]}").val(defaults[item[0]]) if item[1] - window["populate_" + item[1]] + populate_function = "populate_" + item[1] + console.log("Calling:", populate_function) + window[populate_function]() diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js index 655aac15..681e4301 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js +++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js @@ -9,7 +9,7 @@ populate_species(); return apply_default(); }; - $.ajax('/static/new/javascript/dataset_menu_structure', { + $.ajax('/static/new/javascript/dataset_menu_structure.json', { dataType: 'json', success: process_json }); @@ -19,6 +19,7 @@ redo_dropdown($('#species'), species_list); return populate_group(); }; + window.populate_species = populate_species; populate_group = function() { var group_list, species; console.log("in populate group"); @@ -27,6 +28,7 @@ redo_dropdown($('#group'), group_list); return populate_type(); }; + window.populate_group = populate_group; populate_type = function() { var group, species, type_list; species = $('#species').val(); @@ -35,6 +37,7 @@ redo_dropdown($('#type'), type_list); return populate_dataset(); }; + window.populate_type = populate_type; populate_dataset = function() { var dataset_list, group, species, type; species = $('#species').val(); @@ -45,6 +48,7 @@ console.log("pop_dataset:", dataset_list); return redo_dropdown($('#dataset'), dataset_list); }; + window.populate_dataset = populate_dataset; redo_dropdown = function(dropdown, items) { var item, _i, _len, _results; console.log("in redo:", dropdown, items); @@ -99,7 +103,7 @@ }); }; apply_default = function() { - var defaults, item, _i, _len, _ref, _results; + var defaults, item, populate_function, _i, _len, _ref, _results; defaults = $.cookie('search_defaults'); if (!defaults) { return; @@ -111,7 +115,9 @@ item = _ref[_i]; $("#" + item[0]).val(defaults[item[0]]); if (item[1]) { - _results.push(window["populate_" + item[1]]); + populate_function = "populate_" + item[1]; + console.log("Calling:", populate_function); + _results.push(window[populate_function]()); } else { _results.push(void 0); } -- cgit v1.2.3