diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 8 | ||||
| -rw-r--r-- | wqflask/maintenance/generate_probesetfreeze_file.py | 123 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 664 |
3 files changed, 476 insertions, 319 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 0b3b5248..c6d67e68 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -29,8 +29,6 @@ import itertools from flask import Flask, g -from htmlgen import HTMLgen2 as HT - import reaper from base import webqtlConfig @@ -252,11 +250,7 @@ class DataSet(object): #self.cursor.execute(query) #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone() - - - #def genHTML(self, Class='c0dd'): - # return HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class), - # url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank") + class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py new file mode 100644 index 00000000..95515cea --- /dev/null +++ b/wqflask/maintenance/generate_probesetfreeze_file.py @@ -0,0 +1,123 @@ +#!/usr/bin/python + +from __future__ import absolute_import, print_function, division + +import sys + +sys.path.insert(0, "..") + +import os +import collections +import csv + +import MySQLdb + +from base import webqtlConfig + +from pprint import pformat as pf + + +def get_cursor(): + con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME, + host=webqtlConfig.MYSQL_UPDSERVER, + user=webqtlConfig.DB_UPDUSER, + passwd=webqtlConfig.DB_UPDPASSWD) + cursor = con.cursor() + return cursor + +def show_progress(process, counter): + if counter % 1000 == 0: + print("{}: {}".format(process, counter)) + +def get_strains(cursor): + cursor.execute("""select Strain.Name + from Strain, StrainXRef, InbredSet + where Strain.Id = StrainXRef.StrainId and + StrainXRef.InbredSetId = InbredSet.Id + and InbredSet.Name=%s; + """, "BXD") + + strains = [strain[0] for strain in cursor.fetchall()] + print("strains:", pf(strains)) + for strain in strains: + print(" -", strain) + + return strains + +def get_probeset_vals(cursor, dataset_name): + cursor.execute(""" select ProbeSet.Id, ProbeSet.Name + from ProbeSetXRef, + ProbeSetFreeze, + ProbeSet + where ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and + ProbeSetFreeze.Name = %s and + ProbeSetXRef.ProbeSetId = ProbeSet.Id; + """, dataset_name) + + probesets = cursor.fetchall() + + print("Fetched probesets") + + probeset_vals = collections.OrderedDict() + + for counter, probeset in enumerate(probesets): + cursor.execute(""" select Strain.Name, ProbeSetData.value + from ProbeSetData, ProbeSetXRef, ProbeSetFreeze, Strain + where ProbeSetData.Id = ProbeSetXRef.DataId + and ProbeSetData.StrainId = Strain.Id + and ProbeSetXRef.ProbeSetId = %s + and ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId + and ProbeSetFreeze.Name = %s; + """, (probeset[0], dataset_name)) + val_dic = collections.OrderedDict() + vals = cursor.fetchall() + for val in vals: + val_dic[val[0]] = val[1] + + probeset_vals[probeset[1]] = val_dic + show_progress("Querying DB", counter) + + return probeset_vals + +def trim_strains(strains, probeset_vals): + trimmed_strains = [] + #print("probeset_vals is:", pf(probeset_vals)) + first_probeset = list(probeset_vals.itervalues())[0] + for strain in strains: + print("\n**** strain is:", pf(strain)) + print("\n**** first_probeset is:", pf(first_probeset)) + if strain in first_probeset: + trimmed_strains.append(strain) + print("trimmed_strains:", pf(trimmed_strains)) + return trimmed_strains + +def write_data_matrix_file(strains, probeset_vals, filename): + with open(filename, "wb") as fh: + csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL) + #print("strains is:", pf(strains)) + csv_writer.writerow(['ID'] + strains) + for counter, probeset in enumerate(probeset_vals): + row_data = [probeset] + for strain in strains: + #print("probeset is: ", pf(probeset_vals[probeset])) + row_data.append(probeset_vals[probeset][strain]) + #print("row_data is: ", pf(row_data)) + csv_writer.writerow(row_data) + show_progress("Writing", counter) + +def main(): + filename = os.path.expanduser("~/gene/wqflask/maintenance/" + + "ProbeSetFreezeId_379_FullName_EPFL_LISP_BXD_CD_Muscle_Affy_Mouse_Gene_1.0_ST_" + + "(Dec11)_RMA_**.txt") + dataset_name = "EPFLMouseMuscleCDRMA1211" + + cursor = get_cursor() + strains = get_strains(cursor) + print("Getting probset_vals") + probeset_vals = get_probeset_vals(cursor, dataset_name) + print("Finished getting probeset_vals") + trimmed_strains = trim_strains(strains, probeset_vals) + write_data_matrix_file(trimmed_strains, probeset_vals, filename) + +if __name__ == '__main__': + main() diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 898ffa02..88bdcb11 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -64,14 +64,14 @@ ], "Leaf": [ [ - "B1LI0809R", - "Barley1 Leaf INOC TTKS (Aug09) RMA" - ], - [ "B1LI0809M5", "Barley1 Leaf INOC TTKS (Aug09) MAS5" ], [ + "B1LI0809R", + "Barley1 Leaf INOC TTKS (Aug09) RMA" + ], + [ "B1MI0809M5", "Barley1 Leaf MOCK TTKS (Aug09) MAS5" ], @@ -114,12 +114,12 @@ "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)" + ], + [ + "B30_K_1206_Rn", + "Barley1 Leaf gcRMAn SCRI (Dec06)" ] ], "Phenotypes": [ @@ -212,14 +212,14 @@ "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_A_RI_0409", + "GSE15222 Human Brain Alzheimer Myers (Apr09) RankInv" + ], + [ "GSE15222_F_RI_0409", "GSE15222 Human Brain Myers (Apr09) RankInv" ] @@ -381,43 +381,19 @@ "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 **" + "GN330 Human Amygdala 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 **" + "Human Cerebellar Cortex 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 **" + "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], "Genotypes": [ @@ -429,55 +405,31 @@ "Hippocampus": [ [ "KIN_YSM_HIP_0711", - "KIN/YSM Human HIP Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + "Human Hippocampus 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 **" + "Human Inferior Temporal Cortex 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 **" + "Human Medial Prefrontal Cortex 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 **" + "Human Mediodorsal Nucleus of Thalamus 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 **" + "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], "Phenotypes": [ @@ -489,67 +441,49 @@ "Posterior Inferior Parietal Cortex": [ [ "KIN_YSM_IPC_0711", - "KIN/YSM Human IPC Affy Hu-Exon 1.0 ST (Jul11) Quantile **" + "Human Posterior Inferior Parietal Cortex 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 **" + "Human Posterior Superior Temporal Cortex 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 **" + "Human Primary Auditory (A1) Cortex 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 **" + "Human Primary Motor (M1) Cortex 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 **" + "Human Primary Somatosensory (S1) Cortex 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 **" + "Human Primary Visual Cortex 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 **" + "Human Striatum 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 **" + "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ] } @@ -558,12 +492,8 @@ "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 **" + "INIA_MacFas_AMG_RMA_0110", + "INIA Macaca fasicularis Amygdala (Jan10) RMA **" ] ], "Brain": [ @@ -581,21 +511,13 @@ "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 **" + "INIA Macaca fasicularis Hippocampus (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 **" + "INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA **" ] ], "Phenotypes": [ @@ -607,11 +529,7 @@ "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 **" + "INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA **" ] ] } @@ -630,12 +548,12 @@ "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" + ], + [ + "MA_M_0704_R", + "NCI Mammary mRNA M430 (July04) RMA" ] ], "Phenotypes": [ @@ -658,6 +576,12 @@ "AXBXA Genotypes" ] ], + "Liver": [ + [ + "GSE16780AB_UCLA_ML0911", + "GSE16780 UCLA Mouse AXB/BXA Liver Affy HT M430A (Sep11) RMA" + ] + ], "Phenotypes": [ [ "AXBXAPublish", @@ -674,12 +598,12 @@ ], "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" + ], + [ + "LVF2_M_0704_R", + "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA" ] ], "Phenotypes": [ @@ -708,12 +632,12 @@ "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" + ], + [ + "BRF2_M_0304_R", + "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA" ] ], "Genotypes": [ @@ -729,6 +653,46 @@ ] ] }, + "B6D2F2-PSU": { + "Genotypes": [ + [ + "B6D2F2-PSUGeno", + "B6D2F2-PSU Genotypes" + ] + ], + "Muscle": [ + [ + "PSU-B6D2F2_0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA **" + ] + ], + "Phenotypes": [ + [ + "B6D2F2-PSUPublish", + "B6D2F2-PSU Published Phenotypes" + ] + ] + }, + "B6D2RI": { + "Genotypes": [ + [ + "B6D2RIGeno", + "B6D2RI Genotypes" + ] + ], + "Hippocampus": [ + [ + "UTHSC_B6D2RI_H_0912", + "UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA **" + ] + ], + "Phenotypes": [ + [ + "B6D2RIPublish", + "B6D2RI Published Phenotypes" + ] + ] + }, "BDF2-1999": { "Genotypes": [ [ @@ -764,44 +728,44 @@ ], "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" + ], + [ + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" ] ] }, "BHF2": { "Adipose": [ [ - "UCLA_BHF2_ADIPOSE_MALE", - "UCLA BHF2 Adipose Male mlratio" - ], - [ "UCLA_BHF2_ADIPOSE_FEMALE", "UCLA BHF2 Adipose Female mlratio" ], [ + "UCLA_BHF2_ADIPOSE_MALE", + "UCLA BHF2 Adipose Male 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_MALE", + "UCLA BHF2 Brain Male mlratio" + ], + [ "UCLA_BHF2_BRAIN_0605", "UCLA BHF2 Brain (June05) mlratio" ] @@ -814,28 +778,28 @@ ], "Liver": [ [ - "UCLA_BHF2_LIVER_MALE", - "UCLA BHF2 Liver Male mlratio" - ], - [ "UCLA_BHF2_LIVER_FEMALE", "UCLA BHF2 Liver Female mlratio" ], [ + "UCLA_BHF2_LIVER_MALE", + "UCLA BHF2 Liver Male 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_MALE", + "UCLA BHF2 Muscle Male mlratio **" + ], + [ "UCLA_BHF2_MUSCLE_0605", "UCLA BHF2 Muscle (June05) mlratio **" ] @@ -850,30 +814,30 @@ "BHHBF2": { "Adipose": [ [ + "UCLA_BHHBF2_ADIPOSE_2005", + "UCLA BHHBF2 Adipose (2005) 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 **" ] ], "Brain": [ [ + "UCLA_BHHBF2_BRAIN_2005", + "UCLA BHHBF2 Brain (2005) mlratio" + ], + [ "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": [ @@ -884,30 +848,30 @@ ], "Liver": [ [ + "UCLA_BHHBF2_LIVER_2005", + "UCLA BHHBF2 Liver (2005) mlratio" + ], + [ "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_2005", + "UCLA BHHBF2 Muscle (2005) mlratio" + ], + [ "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": [ @@ -918,6 +882,16 @@ ] }, "BXD": { + "Adrenal Gland": [ + [ + "INIA_Adrenal_RMA_0612", + "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA" + ], + [ + "INIA_Adrenal_RMA_Ex_0612", + "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA Exon Level" + ] + ], "Amygdala": [ [ "INIA_AmgCoh_0311", @@ -934,6 +908,10 @@ [ "INIA_Amg_BLA_RMA_F_1110", "INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA Female" + ], + [ + "INIA_Amg_BLA_Ex-RMA_1110", + "INIA Amygdala Exon Affy MoGene 1.0 ST (Nov10) RMA" ] ], "Brain": [ @@ -946,10 +924,6 @@ "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" ], @@ -958,6 +932,10 @@ "UTHSC Brain mRNA U74Av2 (Aug05) PDNN" ], [ + "BR_U_0805_M", + "UTHSC Brain mRNA U74Av2 (Aug05) MAS5" + ], + [ "CB_M_0204_P", "INIA Brain mRNA M430 (Feb04) PDNN" ] @@ -978,10 +956,6 @@ ], "Cerebellum": [ [ - "CB_M_1004_M", - "SJUT Cerebellum mRNA M430 (Oct04) MAS5" - ], - [ "CB_M_1004_R", "SJUT Cerebellum mRNA M430 (Oct04) RMA" ], @@ -990,6 +964,10 @@ "SJUT Cerebellum mRNA M430 (Oct04) PDNN" ], [ + "CB_M_1004_M", + "SJUT Cerebellum mRNA M430 (Oct04) MAS5" + ], + [ "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" ] @@ -1000,6 +978,10 @@ "Eye M430v2 (Sep08) RMA" ], [ + "gn10", + "Eye M430v2 No Mutant/Mutant (Aug12) RMA **" + ], + [ "Eye_M2_0908_R_NB", "Eye M430v2 Mutant Gpnmb (Sep08) RMA **" ], @@ -1008,14 +990,14 @@ "Eye M430v2 WT Gpnmb (Sep08) RMA **" ], [ - "Eye_M2_0908_WTWT", - "Eye M430v2 WT WT (Sep08) RMA **" - ], - [ "Eye_M2_0908_R_MT", "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" ], [ + "Eye_M2_0908_WTWT", + "Eye M430v2 WT WT (Sep08) RMA **" + ], + [ "Eye_M2_0908_R_WT", "Eye M430v2 WT Tyrp1 (Sep08) RMA **" ], @@ -1104,6 +1086,14 @@ [ "UT_ILM_BXD_hipp_RSE_0909", "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" + ], + [ + "UTHSC_BXD_HArev3_0912", + "UTHSC BXD Aged Hippocampus rev3 Affy Mouse Gene 1.0 ST (Sep12) RMA **" + ], + [ + "UTHSC_BXD_H_0912", + "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA Exon Level **" ] ], "Hypothalamus": [ @@ -1118,6 +1108,10 @@ [ "INIA_Hyp_F_RMA_1110", "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10) Female" + ], + [ + "INIA_Hyp_RMA_Ex-1110", + "INIA Hypothalamus Exon Affy MoGene 1.0 ST (Nov10)" ] ], "Kidney": [ @@ -1138,12 +1132,12 @@ "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" + ], + [ + "MA_M2_0706_P", + "Mouse Kidney M430v2 (Jul06) PDNN" ] ], "Leucocytes": [ @@ -1158,6 +1152,18 @@ "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" ], [ + "GenEx_BXD_liverEt_M5_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes **" + ], + [ + "GenEx_BXD_liverEt_M5F_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **" + ], + [ + "GenEx_BXD_liverEt_M5M_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males **" + ], + [ "GenEx_BXD_liverSal_RMA_F_0211", "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" ], @@ -1194,18 +1200,22 @@ [ "HZI_0408_M", "HZI Lung M430v2 (Apr08) MAS5" + ], + [ + "HZI_PR8M_Q_0612", + "HZI PR8M-Infected Lungs Agilent4x44 (Apr12) Quantile Females **" ] ], "Midbrain": [ [ - "VUBXDMouseMidBrainQ0212", - "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (Feb12) Quantile" + "VUBXDMouseMidBrainQ0512", + "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **" ] ], "Muscle": [ [ "EPFLMouseMuscleRMA1211", - "EPFL/LISP BXD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" + "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" ], [ "EPFLMouseMuscleHFDRMA1211", @@ -1218,12 +1228,12 @@ ], "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" ], [ - "DevNeocortex_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv **" + "DevNeocortex_ILM6.2P14RInv_1111", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv" ], [ "HQFNeoc_1210v2_RankInv", @@ -1238,12 +1248,12 @@ "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" ], [ - "DevNeocortex_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv **" + "DevNeocortex_ILM6.2P3RInv_1110", + "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv" ] ], "Nucleus Accumbens": [ @@ -1266,12 +1276,24 @@ "BXD Published Phenotypes" ] ], - "Prefrontal Cortex": [ + "Pituitary Gland": [ [ - "VCUEtOH_1206_R", - "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" + "INIA_PG_RMA_0612", + "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA" ], [ + "INIA_PG_RMA_Ex_0612", + "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Exon Level" + ] + ], + "Popliteal Lymph Node": [ + [ + "STJ_PLN_0912", + "St Jude BXD Popliteal Lymph Node Affy HT MG-430 PM (Sep12) RMA **" + ] + ], + "Prefrontal Cortex": [ + [ "VCUSal_1206_R", "VCU BXD PFC Sal M430 2.0 (Dec06) RMA" ], @@ -1280,6 +1302,10 @@ "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" ], [ + "VCUEtOH_1206_R", + "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA" + ], + [ "VCU_PF_Air_0111_R", "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" ], @@ -1294,16 +1320,20 @@ ], "Retina": [ [ - "Illum_Retina_BXD_RankInv0410", - "HEI Retina Illumina V6.2 (April 2010) RankInv" + "G2NEI_ILM_Retina_BXD_RI0410", + "Normal HEI Retina (April 2010) RankInv" ], [ - "B6D2ONCILM_0412", - "B6D2 ONC Illumina v6.1 (Apr12) RankInv **" + "Illum_Retina_BXD_RankInv0410", + "Full HEI Retina (April 2010) RankInv" ], [ "ONCRetILM6_0412", - "ONC Retina Illumina V6.2 (Apr12) RankInv **" + "ONC HEI Retina (April 2012) RankInv" + ], + [ + "B6D2ONCILM_0412", + "B6D2 ONC Retina (April 2012) RankInv **" ], [ "HEIONCvsCRetILM6_0911", @@ -1312,26 +1342,6 @@ [ "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": [ @@ -1340,32 +1350,40 @@ "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" ], [ + "UTHSC_SPL_RMA_1210M", + "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Males" + ], + [ + "UTHSC_SPL_RMA_1210F", + "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Females" + ], + [ "UTHSC_SPL_RMA_1010", "UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA" ], [ + "UTK_BXDSpl_VST_0110", + "UTK Spleen ILM6.1 (Jan10) VST" + ], + [ "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 **" ], [ + "DevStriatum_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" + ], + [ "UTHSC_Striatum_RankInv_1210", "HQF BXD Striatum ILM6.1 (Dec10v2) RankInv" ], @@ -1430,16 +1448,16 @@ ], "Ventral Tegmental Area": [ [ - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" - ], - [ "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" ], [ "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 **" ] ] }, @@ -1464,6 +1482,12 @@ "BXH Genotypes" ] ], + "Liver": [ + [ + "GSE16780BXH_UCLA_ML0911", + "GSE16780 UCLA Mouse BXH Liver Affy HT M430A (Sep11) RMA" + ] + ], "Phenotypes": [ [ "BXHPublish", @@ -1474,30 +1498,30 @@ "CTB6F2": { "Adipose": [ [ - "UCLA_CTB6B6CTF2_ADIPOSE_MALE", - "UCLA CTB6B6CTF2 Adipose Male mlratio **" + "UCLA_CTB6B6CTF2_ADIPOSE_2005", + "UCLA CTB6/B6CTF2 Adipose (2005) mlratio" ], [ "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE", "UCLA CTB6B6CTF2 Adipose Female mlratio **" ], [ - "UCLA_CTB6B6CTF2_ADIPOSE_2005", - "UCLA CTB6/B6CTF2 Adipose (2005) mlratio **" + "UCLA_CTB6B6CTF2_ADIPOSE_MALE", + "UCLA CTB6B6CTF2 Adipose Male mlratio **" ] ], "Brain": [ [ - "UCLA_CTB6B6CTF2_BRAIN_MALE", - "UCLA CTB6B6CTF2 Brain Male mlratio **" + "UCLA_CTB6B6CTF2_BRAIN_2005", + "UCLA CTB6/B6CTF2 Brain (2005) mlratio" ], [ "UCLA_CTB6B6CTF2_BRAIN_FEMALE", "UCLA CTB6B6CTF2 Brain Female mlratio **" ], [ - "UCLA_CTB6B6CTF2_BRAIN_2005", - "UCLA CTB6/B6CTF2 Brain (2005) mlratio **" + "UCLA_CTB6B6CTF2_BRAIN_MALE", + "UCLA CTB6B6CTF2 Brain Male mlratio **" ] ], "Genotypes": [ @@ -1508,30 +1532,30 @@ ], "Liver": [ [ - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" + "UCLA_CTB6B6CTF2_LIVER_2005", + "UCLA CTB6/B6CTF2 Liver (2005) mlratio" ], [ "UCLA_CTB6B6CTF2_LIVER_FEMALE", "UCLA CTB6B6CTF2 Liver Female mlratio **" ], [ - "UCLA_CTB6B6CTF2_LIVER_2005", - "UCLA CTB6/B6CTF2 Liver (2005) mlratio **" + "UCLA_CTB6B6CTF2_LIVER_MALE", + "UCLA CTB6B6CTF2 Liver Male mlratio **" ] ], "Muscle": [ [ - "UCLA_CTB6B6CTF2_MUSCLE_MALE", - "UCLA CTB6B6CTF2 Muscle Male mlratio **" + "UCLA_CTB6B6CTF2_MUSCLE_2005", + "UCLA CTB6/B6CTF2 Muscle (2005) mlratio" ], [ "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", "UCLA CTB6B6CTF2 Muscle Female mlratio **" ], [ - "UCLA_CTB6B6CTF2_MUSCLE_2005", - "UCLA CTB6/B6CTF2 Muscle (2005) mlratio **" + "UCLA_CTB6B6CTF2_MUSCLE_MALE", + "UCLA CTB6B6CTF2 Muscle Male mlratio **" ] ], "Phenotypes": [ @@ -1550,12 +1574,12 @@ ], "Hippocampus": [ [ - "HC_M2CB_1205_R", - "Hippocampus Consortium M430v2 CXB (Dec05) RMA" - ], - [ "HC_M2CB_1205_P", "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" + ], + [ + "HC_M2CB_1205_R", + "Hippocampus Consortium M430v2 CXB (Dec05) RMA" ] ], "Phenotypes": [ @@ -1660,10 +1684,6 @@ "Hippocampus Illumina (May07) RankInv" ], [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ], - [ "Illum_LXS_Hipp_RSE_1008", "Hippocampus Illumina RSE (Oct08) RankInv beta" ], @@ -1678,6 +1698,10 @@ [ "Illum_LXS_Hipp_NOS_1008", "Hippocampus Illumina NOS (Oct08) RankInv beta" + ], + [ + "Illum_LXS_Hipp_NON_1008", + "Hippocampus Illumina NON (Oct08) RankInv beta" ] ], "Phenotypes": [ @@ -1688,16 +1712,16 @@ ], "Prefrontal Cortex": [ [ - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], - [ "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" ], [ "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 **" ] ] }, @@ -1710,16 +1734,20 @@ ], "Hippocampus": [ [ - "UMUTAffyExon_0209_RMA_MDP", - "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" - ], - [ "HC_M2_0606_MDP", "Hippocampus Consortium M430v2 (Jun06) RMA MDP" + ], + [ + "UMUTAffyExon_0209_RMA_MDP", + "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" ] ], "Liver": [ [ + "GSE16780MDP_UCLA_ML0911", + "GSE16780 UCLA Mouse MDP Liver Affy HT M430A (Sep11) RMA" + ], + [ "JAX_CSB_L_0711", "JAX Liver Affy M430 2.0 (Jul11) MDP" ], @@ -1921,19 +1949,19 @@ "human": [ [ "AD-cases-controls", - "AD Cases & Controls (Liang)" + "Alzheimer's Disease Brain (Liang)" ], [ "AD-cases-controls-Myers", - "AD Cases & Controls (Myers)" + "Alzheimer's Disease Brain (Myers)" ], [ "CANDLE", - "CANDLE" + "CANDLE Cognitive Development (TUCI)" ], [ "CEPH-2004", - "CEPH Families" + "CEPH Families Cell Lines" ], [ "HB", @@ -1941,11 +1969,11 @@ ], [ "HLC", - "Human Liver Cohort" + "Human Liver Cohort (Merck)" ], [ "HSB", - "KIN/YSM" + "Human Brain Transcriptome (Yale/Kavli)" ] ], "macaque monkey": [ @@ -1972,6 +2000,14 @@ "B6D2F2" ], [ + "B6D2F2-PSU", + "B6D2F2 PSU" + ], + [ + "B6D2RI", + "B6D2RI Aged" + ], + [ "BDF2-1999", "BDF2 UCLA" ], @@ -2301,30 +2337,14 @@ "Amygdala mRNA" ], [ - "Caudal Ganglionic Eminence", - "Caudal Ganglionic Eminence mRNA" - ], - [ "Cerebellar Cortex", "Cerebellar Cortex mRNA" ], [ - "Diencephalon", - "Diencephalon mRNA" - ], - [ - "Dorsal Thalamus", - "Dorsal Thalamus mRNA" - ], - [ "Dorsolateral Prefrontal Cortex", "Dorsolateral Prefrontal Cortex mRNA" ], [ - "Frontal Cerebral Wall", - "Frontal Cerebral Wall mRNA" - ], - [ "Hippocampus", "Hippocampus mRNA" ], @@ -2333,14 +2353,6 @@ "Inferior Temporal Cortex mRNA" ], [ - "Lateral Ganglionic Eminence", - "Lateral Ganglionic Eminence mRNA" - ], - [ - "Medial Ganglionic Eminence", - "Medial Ganglionic Eminence mRNA" - ], - [ "Medial Prefrontal Cortex", "Medial Prefrontal Cortex mRNA" ], @@ -2349,18 +2361,10 @@ "Mediodorsal Nucleus of Thalamus mRNA" ], [ - "Occipital Cerebral Wall", - "Occipital Cerebral Wall mRNA" - ], - [ "Orbital Prefrontal Cortex", "Orbital Prefrontal Cortex mRNA" ], [ - "Parietal Cerebral Wall", - "Parietal Cerebral Wall mRNA" - ], - [ "Posterior Inferior Parietal Cortex", "Posterior Inferior Parietal Cortex mRNA" ], @@ -2389,18 +2393,6 @@ "Striatum mRNA" ], [ - "Temporal Cerebral Wall", - "Temporal Cerebral Wall mRNA" - ], - [ - "Upper (Rostral) Rhombic Lip", - "Upper (Rostral) Rhombic Lip mRNA" - ], - [ - "Ventral Forebrain", - "Ventral Forebrain mRNA" - ], - [ "Ventrolateral Prefrontal Cortex", "Ventrolateral Prefrontal Cortex mRNA" ] @@ -2465,6 +2457,10 @@ [ "Eye", "Eye mRNA" + ], + [ + "Liver", + "Liver mRNA" ] ], "B6BTBRF2": [ @@ -2495,6 +2491,34 @@ "Brain mRNA" ] ], + "B6D2F2-PSU": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Muscle", + "Muscle mRNA" + ] + ], + "B6D2RI": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Hippocampus", + "Hippocampus mRNA" + ] + ], "BDF2-1999": [ [ "Phenotypes", @@ -2585,6 +2609,10 @@ "Genotypes" ], [ + "Adrenal Gland", + "Adrenal Gland mRNA" + ], + [ "Amygdala", "Amygdala mRNA" ], @@ -2649,6 +2677,14 @@ "Nucleus Accumbens mRNA" ], [ + "Pituitary Gland", + "Pituitary Gland mRNA" + ], + [ + "Popliteal Lymph Node", + "Popliteal Lymph Node mRNA" + ], + [ "Prefrontal Cortex", "Prefrontal Cortex mRNA" ], @@ -2693,6 +2729,10 @@ [ "Cartilage", "Cartilage mRNA" + ], + [ + "Liver", + "Liver mRNA" ] ], "CTB6F2": [ |