diff options
| -rw-r--r-- | misc/gn_installation_notes.txt | 7 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfig.py | 3 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfigLocal.py | 20 | ||||
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 55 | ||||
| l--------- | wqflask/maintenance/our_settings.py | 1 | ||||
| -rw-r--r-- | wqflask/secure_server.py | 3 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 1330 |
7 files changed, 950 insertions, 469 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt index 46441b39..d32faad7 100644 --- a/misc/gn_installation_notes.txt +++ b/misc/gn_installation_notes.txt @@ -162,6 +162,13 @@ service mysql stop ============================================ +Check RSA key: +ssh-keygen -l -f /etc/ssh/ssh_host_rsa_key + +03:2c:d7:01:01:f0:31:3a:c8:df:e4:98:62:2c:59:d2 root@penguin (RSA) + +============================================ + Using Yolk Install Yolk: diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index a811c3cd..716986db 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -1,4 +1,3 @@ -from webqtlConfigLocal import * #########################################' # Environment Variables - public ######################################### @@ -49,6 +48,8 @@ UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit" ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" + +GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'web/' diff --git a/wqflask/base/webqtlConfigLocal.py b/wqflask/base/webqtlConfigLocal.py deleted file mode 100755 index abaeff93..00000000 --- a/wqflask/base/webqtlConfigLocal.py +++ /dev/null @@ -1,20 +0,0 @@ -#########################################' -# Environment Variables - private -######################################### - -MYSQL_SERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com' -DB_NAME = 'db_webqtl' -DB_USER = 'webqtl' -DB_PASSWD = 'f2ZypIflRM' - -MYSQL_UPDSERVER = 'gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com' -DB_UPDNAME = 'db_webqtl' -DB_UPDUSER = 'webqtl' -DB_UPDPASSWD = 'f2ZypIflRM' - -GNROOT = '/home/zas1024/gene/' -ROOT_URL = 'http://50.16.251.170' -PythonPath = '/usr/bin/python' -PIDDLE_FONT_PATH = '/usr/lib/python2.4/site-packages/piddle/truetypefonts/' - -TEXTUI=1 # XZ: This is to protect GN production server. If set to 0, no text UI is allowed. diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 4c544192..acf21ed8 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -29,25 +29,47 @@ It needs to be run manually when database has been changed. from __future__ import print_function, division -import sys +#from flask import config +# +#cdict = {} +#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS') +#print("cdict is:", cdict) -sys.path.insert(0, "..") +import our_settings import MySQLdb import simplejson as json +import urlparse -from pprint import pformat as pf -from base import webqtlConfig +#import sqlalchemy as sa + +from pprint import pformat as pf +#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI) # 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() + +#conn = Engine.connect() + + + + + +def parse_db_uri(db_uri): + """Converts a database URI to the db name, host name, user name, and password""" + + parsed_uri = urlparse.urlparse(our_settings.DB_URI) + + db_conn_info = dict( + db = parsed_uri.path[1:], + host = parsed_uri.hostname, + user = parsed_uri.username, + passwd = parsed_uri.password) + + return db_conn_info + def get_species(): @@ -100,8 +122,8 @@ def build_types(species, group): ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and - ProbeSetFreeze.public > %s - order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH)) + ProbeSetFreeze.public > 0 + order by Tissue.Name""", (species, group)) return Cursor.fetchall() @@ -140,14 +162,17 @@ def build_datasets(species, group, type_name): 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 + InbredSet.Id and ProbeSetFreeze.public > 0 order by ProbeSetFreeze.CreateTime desc""", ( - species, group, type_name, webqtlConfig.PUBLICTHRESH)) + species, group, type_name)) return Cursor.fetchall() def main(): """Generates and outputs (as json file) the data for the main dropdown menus on the home page""" + + parse_db_uri(our_settings.DB_URI) + species = get_species() groups = get_groups(species) types = get_types(groups) @@ -182,5 +207,7 @@ def _test_it(): datasets = build_datasets("Mouse", "BXD", "Hippocampus") print("build_datasets:", pf(datasets)) -if __name__ == '__main__': +if __name__ == '__main__': + Conn = MySQLdb.Connect(**parse_db_uri(our_settings.DB_URI)) + Cursor = Conn.cursor() main() diff --git a/wqflask/maintenance/our_settings.py b/wqflask/maintenance/our_settings.py new file mode 120000 index 00000000..14efe407 --- /dev/null +++ b/wqflask/maintenance/our_settings.py @@ -0,0 +1 @@ +../../../zach_settings.py \ No newline at end of file diff --git a/wqflask/secure_server.py b/wqflask/secure_server.py index 3487f35b..2abfdb05 100644 --- a/wqflask/secure_server.py +++ b/wqflask/secure_server.py @@ -4,12 +4,10 @@ from wqflask import app from flask import Flask, render_template - # Setup mail from flask.ext.mail import Mail mail = Mail(app) - from wqflask.model import * # Create a user to test with @@ -19,7 +17,6 @@ from wqflask.model import * # user_datastore.create_user(email='matt@example.com', password='notebook') # db.session.commit() - import logging file_handler = logging.FileHandler(app.config['LOGFILE']) file_handler.setLevel(logging.DEBUG) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 88bdcb11..4aae20ba 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -62,16 +62,16 @@ "QSM Genotypes" ] ], - "Leaf": [ - [ - "B1LI0809M5", - "Barley1 Leaf INOC TTKS (Aug09) MAS5" - ], + "Leaf mRNA": [ [ "B1LI0809R", "Barley1 Leaf INOC TTKS (Aug09) RMA" ], [ + "B1LI0809M5", + "Barley1 Leaf INOC TTKS (Aug09) MAS5" + ], + [ "B1MI0809M5", "Barley1 Leaf MOCK TTKS (Aug09) MAS5" ], @@ -88,7 +88,7 @@ ] }, "SXM": { - "Embryo": [ + "Embryo mRNA": [ [ "B139_K_1206_R", "Barley1 Embryo gcRMA SCRI (Dec06)" @@ -108,18 +108,18 @@ "SXM Genotypes" ] ], - "Leaf": [ + "Leaf mRNA": [ [ "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": [ @@ -144,7 +144,7 @@ "DGRP Published Phenotypes" ] ], - "Whole Body": [ + "Whole Body mRNA": [ [ "NCSU_DrosWB_LC_RMA_0111", "NCSU Drosophila Whole Body (Jan11) RMA" @@ -164,7 +164,7 @@ "Oregon-R_x_2b3 Published Phenotypes" ] ], - "Whole Body": [ + "Whole Body mRNA": [ [ "UAB_DrosWB_LC_RMA_1009", "UAB Whole body D.m. mRNA control (Oct09) RMA" @@ -178,7 +178,7 @@ }, "human": { "AD-cases-controls": { - "Brain": [ + "Brain mRNA": [ [ "GSE5281_F_RMA_N_0709", "GSE5281 Human Brain Normal Full Liang (Jul09) RMA" @@ -210,16 +210,16 @@ ] }, "AD-cases-controls-Myers": { - "Brain": [ - [ - "GSE15222_F_N_RI_0409", - "GSE15222 Human Brain Normal Myers (Apr09) RankInv" - ], + "Brain mRNA": [ [ "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" ] @@ -244,10 +244,20 @@ "CANDLE Genotypes" ] ], - "Newborn Cord Blood": [ + "Methylation": [ + [ + "CANDLE_Meth27_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) **" + ], + [ + "CANDLE_Meth_0313", + "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) Z-Score **" + ] + ], + "Newborn Cord Blood mRNA": [ [ "CANDLE_NB_0711", - "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT **" + "CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT" ] ], "Phenotypes": [ @@ -264,7 +274,7 @@ "CEPH-2004 Genotypes" ] ], - "Lymphoblast B-cell": [ + "Lymphoblast B-cell mRNA": [ [ "UT_CEPH_RankInv0909", "UTHSC CEPH B-cells Illumina (Sep09) RankInv" @@ -282,7 +292,7 @@ ] }, "HB": { - "Cerebellum": [ + "Cerebellum mRNA": [ [ "HBTRC-MLC_0611", "HBTRC-MLC Human Cerebellum Agilent (Jun11) mlratio" @@ -312,7 +322,7 @@ "HB Published Phenotypes" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ [ "HBTRC-MLPFC_0611", "HBTRC-MLC Human Prefrontal Cortex Agilent (Jun11) mlratio" @@ -330,7 +340,7 @@ "HBTRC-MLC Human Prefrontal Cortex Agilent HD (Jun11) mlratio" ] ], - "Primary Visual Cortex": [ + "Primary Visual Cortex mRNA": [ [ "HBTRC-MLVC_0611", "HBTRC-MLC Human Visual Cortex Agilent (Jun11) mlratio" @@ -356,7 +366,7 @@ "HLC Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "HLC_0311", "GSE9588 Human Liver Normal (Mar11) Both Sexes" @@ -377,20 +387,52 @@ ] ] }, + "HLT": { + "Genotypes": [ + [ + "HLTGeno", + "HLT Genotypes" + ] + ], + "Lung mRNA": [ + [ + "GSE23546HLT0613", + "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ], + [ + "luCA_GSE23352HLT0613", + "UL/GSE23352 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA (Jun11) RMA" + ], + [ + "UBC-GSE23529HLT0613", + "UBC/GSE23529 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ], + [ + "GRNG-GSE23545HLT0613", + "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" + ] + ], + "Phenotypes": [ + [ + "HLTPublish", + "HLT Published Phenotypes" + ] + ] + }, "HSB": { - "Amygdala": [ + "Amygdala mRNA": [ [ "KIN_YSM_AMY_0711", "GN330 Human Amygdala Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Cerebellar Cortex": [ + "Cerebellar Cortex mRNA": [ [ "KIN_YSM_CBC_0711", "Human Cerebellar Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Dorsolateral Prefrontal Cortex": [ + "Dorsolateral Prefrontal Cortex mRNA": [ [ "KIN_YSM_DFC_0711", "Human Dorsolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" @@ -402,31 +444,31 @@ "HSB Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "KIN_YSM_HIP_0711", "Human Hippocampus Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Inferior Temporal Cortex": [ + "Inferior Temporal Cortex mRNA": [ [ "KIN_YSM_ITC_0711", "Human Inferior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Medial Prefrontal Cortex": [ + "Medial Prefrontal Cortex mRNA": [ [ "KIN_YSM_MFC_0711", "Human Medial Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Mediodorsal Nucleus of Thalamus": [ + "Mediodorsal Nucleus of Thalamus mRNA": [ [ "KIN_YSM_MD_0711", "Human Mediodorsal Nucleus of Thalamus Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Orbital Prefrontal Cortex": [ + "Orbital Prefrontal Cortex mRNA": [ [ "KIN_YSM_OFC_0711", "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" @@ -438,49 +480,49 @@ "HSB Published Phenotypes" ] ], - "Posterior Inferior Parietal Cortex": [ + "Posterior Inferior Parietal Cortex mRNA": [ [ "KIN_YSM_IPC_0711", "Human Posterior Inferior Parietal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Posterior Superior Temporal Cortex": [ + "Posterior Superior Temporal Cortex mRNA": [ [ "KIN_YSM_STC_0711", "Human Posterior Superior Temporal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Auditory (A1) Cortex": [ + "Primary Auditory (A1) Cortex mRNA": [ [ "KIN_YSM_A1C_0711", "Human Primary Auditory (A1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Motor (M1) Cortex": [ + "Primary Motor (M1) Cortex mRNA": [ [ "KIN_YSM_M1C_0711", "Human Primary Motor (M1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Somatosensory (S1) Cortex": [ + "Primary Somatosensory (S1) Cortex mRNA": [ [ "KIN_YSM_S1C_0711", "Human Primary Somatosensory (S1) Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Primary Visual Cortex": [ + "Primary Visual Cortex mRNA": [ [ "KIN_YSM_V1C_0711", "Human Primary Visual Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Striatum": [ + "Striatum mRNA": [ [ "KIN_YSM_STR_0711", "Human Striatum Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], - "Ventrolateral Prefrontal Cortex": [ + "Ventrolateral Prefrontal Cortex mRNA": [ [ "KIN_YSM_VFC_0711", "Human Ventrolateral Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" @@ -490,13 +532,13 @@ }, "macaque monkey": { "Macaca-fasicularis": { - "Amygdala": [ + "Amygdala mRNA": [ [ "INIA_MacFas_AMG_RMA_0110", "INIA Macaca fasicularis Amygdala (Jan10) RMA **" ] ], - "Brain": [ + "Brain mRNA": [ [ "INIA_MacFas_brain_RMA_0110", "INIA Macaca fasicularis Brain (Jan10) RMA **" @@ -508,13 +550,13 @@ "Macaca-fasicularis Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "INIA_MacFas_Hc_RMA_0110", "INIA Macaca fasicularis Hippocampus (Jan10) RMA **" ] ], - "Nucleus Accumbens": [ + "Nucleus Accumbens mRNA": [ [ "INIA_MacFas_Ac_RMA_0110", "INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA **" @@ -526,7 +568,7 @@ "Macaca-fasicularis Published Phenotypes" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ [ "INIA_MacFas_Pf_RMA_0110", "INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA **" @@ -542,18 +584,18 @@ "AKXD Genotypes" ] ], - "Mammary Tumors": [ + "Mammary Tumors mRNA": [ [ "NCI_Agil_Mam_Tum_RMA_0409", "NCI Mammary LMT miRNA v2 (Apr09) RMA" ], [ - "MA_M_0704_M", - "NCI Mammary mRNA M430 (July04) MAS5" - ], - [ "MA_M_0704_R", "NCI Mammary mRNA M430 (July04) RMA" + ], + [ + "MA_M_0704_M", + "NCI Mammary mRNA M430 (July04) MAS5" ] ], "Phenotypes": [ @@ -564,7 +606,13 @@ ] }, "AXBXA": { - "Eye": [ + "Bone Femur mRNA": [ + [ + "UCLA_AXB/BXA_Femur_0113_RSN", + "UCLA GSE27483 AXB/BXA Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ] + ], + "Eye mRNA": [ [ "Eye_AXBXA_1008_RankInv", "Eye AXBXA Illumina V6.2(Oct08) RankInv Beta" @@ -576,7 +624,13 @@ "AXBXA Genotypes" ] ], - "Liver": [ + "Heart mRNA": [ + [ + "IRCM_AXBXA_HRI0213", + "IRCM AXB/BXA Mouse Heart ILM MouseRef-8 v2.0 (Feb13) RankInv" + ] + ], + "Liver mRNA": [ [ "GSE16780AB_UCLA_ML0911", "GSE16780 UCLA Mouse AXB/BXA Liver Affy HT M430A (Sep11) RMA" @@ -596,14 +650,14 @@ "B6BTBRF2 Genotypes" ] ], - "Liver": [ - [ - "LVF2_M_0704_M", - "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5" - ], + "Liver mRNA": [ [ "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": [ @@ -614,7 +668,11 @@ ] }, "B6D2F2": { - "Brain": [ + "Brain mRNA": [ + [ + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + ], [ "BRF2_M_0805_M", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" @@ -624,20 +682,16 @@ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" ], [ - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ "BRF2_M_0304_P", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" ], [ - "BRF2_M_0304_M", - "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5" - ], - [ "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": [ @@ -660,10 +714,22 @@ "B6D2F2-PSU Genotypes" ] ], - "Muscle": [ + "Muscle mRNA": [ [ "PSU-B6D2F2_0812", "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA **" + ], + [ + "PSU-B6D2F2_F0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Females **" + ], + [ + "PSU-B6D2F2_M0812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males **" + ], + [ + "PSU-B6D2F2_M2000812", + "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200 **" ] ], "Phenotypes": [ @@ -680,7 +746,7 @@ "B6D2RI Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "UTHSC_B6D2RI_H_0912", "UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA **" @@ -700,7 +766,7 @@ "BDF2-1999 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "UCLA_BDF2_LIVER_1999", "UCLA BDF2 Liver (1999) mlratio" @@ -726,7 +792,11 @@ "BDF2-2005 Published Phenotypes" ] ], - "Striatum": [ + "Striatum mRNA": [ + [ + "SA_M2_0905_R", + "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA" + ], [ "SA_M2_0905_M", "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5" @@ -734,38 +804,34 @@ [ "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_FEMALE", - "UCLA BHF2 Adipose Female mlratio" - ], + "Adipose mRNA": [ [ "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_FEMALE", - "UCLA BHF2 Brain Female mlratio" - ], + "Brain mRNA": [ [ "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" ] @@ -776,30 +842,30 @@ "BHF2 Genotypes" ] ], - "Liver": [ - [ - "UCLA_BHF2_LIVER_FEMALE", - "UCLA BHF2 Liver Female mlratio" - ], + "Liver mRNA": [ [ "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_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], + "Muscle mRNA": [ [ "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 **" ] @@ -812,7 +878,7 @@ ] }, "BHHBF2": { - "Adipose": [ + "Adipose mRNA": [ [ "UCLA_BHHBF2_ADIPOSE_2005", "UCLA BHHBF2 Adipose (2005) mlratio" @@ -826,7 +892,7 @@ "UCLA BHHBF2 Adipose Female Only" ] ], - "Brain": [ + "Brain mRNA": [ [ "UCLA_BHHBF2_BRAIN_2005", "UCLA BHHBF2 Brain (2005) mlratio" @@ -846,7 +912,7 @@ "BHHBF2 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "UCLA_BHHBF2_LIVER_2005", "UCLA BHHBF2 Liver (2005) mlratio" @@ -860,7 +926,7 @@ "UCLA BHHBF2 Liver Female Only" ] ], - "Muscle": [ + "Muscle mRNA": [ [ "UCLA_BHHBF2_MUSCLE_2005", "UCLA BHHBF2 Muscle (2005) mlratio" @@ -882,17 +948,25 @@ ] }, "BXD": { - "Adrenal Gland": [ + "Adrenal Gland mRNA": [ [ "INIA_Adrenal_RMA_0612", "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA" ], [ + "INIA_Adrenal_RMA_F_0612", + "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA Females" + ], + [ + "INIA_Adrenal_RMA_M_0612", + "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA Males" + ], + [ "INIA_Adrenal_RMA_Ex_0612", "INIA Adrenal Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], - "Amygdala": [ + "Amygdala mRNA": [ [ "INIA_AmgCoh_0311", "INIA Amygdala Cohort Affy MoGene 1.0 ST (Mar11) RMA" @@ -914,7 +988,25 @@ "INIA Amygdala Exon Affy MoGene 1.0 ST (Nov10) RMA" ] ], - "Brain": [ + "Bone Femur mRNA": [ + [ + "UCLA_BXD_Femur_0113_RSN", + "UCLA GSE27483 BXD Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ], + [ + "UCLA_BXD-on_Femur_0113_RSN", + "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v2.0 (Jan13) RSN" + ] + ], + "Brain mRNA": [ + [ + "UTHSC_BXD_WB_RNASeq1112", + "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM" + ], + [ + "UTHSC_BXD_WB_RNASeqEx1112", + "UTHSC Mouse BXD Whole Brain RNA Sequence Exon Level (Nov12) RPKM" + ], [ "BR_M2_1106_R", "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA" @@ -924,6 +1016,10 @@ "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" ], @@ -932,15 +1028,11 @@ "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" ] ], - "Cartilage": [ + "Cartilage mRNA": [ [ "UCLA_BXDBXH_CARTILAGE_V2", "UCLA BXD and BXH Cartilage v2" @@ -954,7 +1046,7 @@ "UCLA BXD Cartilage" ] ], - "Cerebellum": [ + "Cerebellum mRNA": [ [ "CB_M_1004_R", "SJUT Cerebellum mRNA M430 (Oct04) RMA" @@ -970,9 +1062,65 @@ [ "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" + ], + [ + "CMMTUBCBXDCerILM0513", + "UBC/CMMT BXD Cerebellum All Ages Combined ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDG12CerILM0513", + "UBC/CMMT BXD E12 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDG15CerILM0513", + "UBC/CMMT BXD E15 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDG18CerILM0513", + "UBC/CMMT BXD E18 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP00CerILM0513", + "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP03CerILM0513", + "UBC/CMMT BXD P3 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP06CerILM0513", + "UBC/CMMT BXD P6 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "CMMTUBCBXDP09CerILM0513", + "UBC/CMMT BXD P9 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" + ], + [ + "GenEx_BXD_CerebEt_RMA_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes **" + ], + [ + "GenEx_BXD_CerebEt_RMA_F_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Females **" + ], + [ + "GenEx_BXD_CerebEt_RMA_M_0213", + "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Males **" + ], + [ + "GenEx_BXD_CerebSal_RMA_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes **" + ], + [ + "GenEx_BXD_CerebSal_RMA_F_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Females **" + ], + [ + "GenEx_BXD_CerebSal_RMA_M_0213", + "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Males **" ] ], - "Eye": [ + "Eye mRNA": [ [ "Eye_M2_0908_R", "Eye M430v2 (Sep08) RMA" @@ -990,6 +1138,14 @@ "Eye M430v2 WT Gpnmb (Sep08) RMA **" ], [ + "Eye_M2_0908_R_WT", + "Eye M430v2 WT Tyrp1 (Sep08) RMA **" + ], + [ + "DBA2J-ONH-1212", + "ONH BXD Glaucoma Affy M430 2.0 Trial (Dec12) RMA **" + ], + [ "Eye_M2_0908_R_MT", "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" ], @@ -998,10 +1154,6 @@ "Eye M430v2 WT WT (Sep08) RMA **" ], [ - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA **" - ], - [ "BXD_GLA_0911", "BXD Glaucoma Affy M430 2.0 Trial (Sep11) RMA **" ] @@ -1012,7 +1164,7 @@ "BXD Genotypes" ] ], - "Hematopoietic Cells": [ + "Hematopoietic Cells mRNA": [ [ "UMCG_0907_HemaStem_ori", "UMCG Stem Cells ILM6v1.1 (Apr09) original" @@ -1050,7 +1202,7 @@ "GNF Stem Cells U74Av2 (Mar04) RMA" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "HC_M2_0606_P", "Hippocampus Consortium M430v2 (Jun06) PDNN" @@ -1064,6 +1216,30 @@ "Hippocampus Consortium M430v2 (Jun06) RMA" ], [ + "UT_ILM_BXD_hipp_5T_1112", + "UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_NON_1112", + "UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_NOS_1112", + "UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_NOE_1112", + "UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_RSS_1112", + "UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv" + ], + [ + "UT_ILM_BXD_hipp_RSE_1112", + "UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv" + ], + [ "UMUTAffyExon_0209_RMA", "UMUTAffy Hippocampus Exon (Feb09) RMA" ], @@ -1096,7 +1272,7 @@ "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA Exon Level **" ] ], - "Hypothalamus": [ + "Hypothalamus mRNA": [ [ "INIA_Hyp_RMA_1110", "INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)" @@ -1114,16 +1290,16 @@ "INIA Hypothalamus Exon Affy MoGene 1.0 ST (Nov10)" ] ], - "Kidney": [ - [ - "MA_M2M_0706_R", - "Mouse kidney M430v2 Male (Aug06) RMA" - ], + "Kidney mRNA": [ [ "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" ], @@ -1132,67 +1308,109 @@ "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN" ], [ - "MA_M2_0706_R", - "Mouse Kidney M430v2 (Jul06) RMA" - ], - [ "MA_M2_0706_P", "Mouse Kidney M430v2 (Jul06) PDNN" + ], + [ + "MA_M2_0706_R", + "Mouse Kidney M430v2 (Jul06) RMA" ] ], - "Leucocytes": [ + "Leucocytes mRNA": [ [ "Illum_BXD_PBL_1108", "UWA Illumina PBL (Nov08) RSN **" ] ], - "Liver": [ + "Liver Proteome": [ + [ + "EPFLBXDprotRPN0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (May13) RPN **" + ], + [ + "EPFLBXDprotHFDRPN0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins HFD (May13) RPN **" + ], + [ + "EPFLBXDprotCDRPN0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD (May13) RPN **" + ], + [ + "EPFLBXDprot0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD+HFD (May13) **" + ], + [ + "EPFLBXDprotHFD0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins HFD (May13) **" + ], + [ + "EPFLBXDprotCD0513", + "EPFL/LISP BXD Liver, Hepatocytes, Soluable Proteins CD (May13) **" + ] + ], + "Liver mRNA": [ [ "GSE16780_UCLA_ML0911", "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 **" + "EPFLMouseLiverRMA0413", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA **" ], [ - "GenEx_BXD_liverEt_M5F_0912", - "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **" + "EPFLMouseLiverHFDRMA0413", + "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA **" + ], + [ + "EPFLMouseLiverCDRMA0413", + "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA **" + ], + [ + "EPFLMouseLiverBothExRMA0413", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level **" + ], + [ + "GenEx_BXD_liverEt_M5_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes **" ], [ "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 **" + "GenEx_BXD_liverEt_M5F_0912", + "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **" ], [ - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal 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 **" ], [ - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + "GenEx_BXD_liverEt_RMA_M_0211", + "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" ], [ "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_liverSal_RMA_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" ], [ - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" + "GenEx_BXD_liverSal_RMA_M_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" + ], + [ + "GenEx_BXD_liverSal_RMA_F_0211", + "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" ], [ "SUH_Liv_RMA_0611", "SUH BXD Liver Affy Mouse Gene 1.0 ST (Jun11) RMA **" ] ], - "Lung": [ + "Lung mRNA": [ [ "HZI_0408_R", "HZI Lung M430v2 (Apr08) RMA" @@ -1202,17 +1420,33 @@ "HZI Lung M430v2 (Apr08) MAS5" ], [ + "HZI_LTCF_0313", + "HZI Lung Time Course Flu PR8M (Mar13) Schughart **" + ], + [ "HZI_PR8M_Q_0612", "HZI PR8M-Infected Lungs Agilent4x44 (Apr12) Quantile Females **" ] ], - "Midbrain": [ + "Midbrain mRNA": [ [ "VUBXDMouseMidBrainQ0512", "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile **" ] ], - "Muscle": [ + "Muscle mRNA": [ + [ + "EPFLMouseMuscleRMA_Ex1112", + "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level **" + ], + [ + "EPFLMouseMuscleHFDRMAEx1112", + "EPFL/LISP BXD HFD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level **" + ], + [ + "EPFLMouseMuscleCDRMAEx1112", + "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Nov12) RMA Exon Level **" + ], [ "EPFLMouseMuscleRMA1211", "EPFL/LISP BXD CD+HFD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" @@ -1226,16 +1460,16 @@ "EPFL/LISP BXD CD Muscle Affy Mouse Gene 1.0 ST (Dec11) RMA **" ] ], - "Neocortex": [ - [ - "DevNeocortex_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv" - ], + "Neocortex mRNA": [ [ "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" ], @@ -1248,20 +1482,32 @@ "HQF BXD Neocortex ILM6v1.1 (Feb08) 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" + ], + [ + "DevNeocortex_ILM6.2P14RInv_1110", + "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv" ] ], - "Nucleus Accumbens": [ + "Nucleus Accumbens mRNA": [ [ "VCUSalo_1007_R", "VCU BXD NA Sal M430 2.0 (Oct07) RMA" ], [ + "VCU_NAc_AvE_0113_Ss", + "VCU BXD NAc EtOH vs CIE Air M430 2.0 (Jan13) Sscore **" + ], + [ + "VCU_NAc_Et_0113_R", + "VCU BXD NAc CIE EtOH M430 2.0 (Jan13) RMA **" + ], + [ + "VCU_NAc_Air_0113_R", + "VCU BXD NAc CIE Air M430 2.0 (Jan13) RMA **" + ], + [ "VCUEtOH_1007_R", "VCU BXD NA EtOH M430 2.0 (Oct07) RMA **" ], @@ -1276,49 +1522,57 @@ "BXD Published Phenotypes" ] ], - "Pituitary Gland": [ + "Pituitary Gland mRNA": [ [ "INIA_PG_RMA_0612", "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA" ], [ + "INIA_Pituitary_RMA_F_0612", + "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Females" + ], + [ + "INIA_Pituitary_RMA_M_0612", + "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Males" + ], + [ "INIA_PG_RMA_Ex_0612", "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], - "Popliteal Lymph Node": [ + "Popliteal Lymph Node mRNA": [ [ "STJ_PLN_0912", "St Jude BXD Popliteal Lymph Node Affy HT MG-430 PM (Sep12) RMA **" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ [ "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" - ], - [ "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 **" + "VCUSal_1006_R", + "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" + ], + [ + "VCU_PF_AvE_0111_Ss", + "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" ], [ "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 **" + "VCU_PF_Air_0111_R", + "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" ] ], - "Retina": [ + "Retina mRNA": [ [ "G2NEI_ILM_Retina_BXD_RI0410", "Normal HEI Retina (April 2010) RankInv" @@ -1332,6 +1586,14 @@ "ONC HEI Retina (April 2012) RankInv" ], [ + "ONCRetMoGene2_0413", + "DoD TATRC Retina Affy MoGene 2.0 ST (Apr13) RMA **" + ], + [ + "ONCRetExMoGene2_0413", + "DoD TATRC Retina Affy MoGene 2.0 ST (Apr13) RMA Exon Level **" + ], + [ "B6D2ONCILM_0412", "B6D2 ONC Retina (April 2012) RankInv **" ], @@ -1344,7 +1606,7 @@ "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" ] ], - "Spleen": [ + "Spleen mRNA": [ [ "UTHSC_SPL_RMA_1210", "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" @@ -1358,6 +1620,10 @@ "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Females" ], [ + "UTHSC_SPL_RMAEx_1210", + "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Exon Level" + ], + [ "UTHSC_SPL_RMA_1010", "UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA" ], @@ -1374,14 +1640,14 @@ "UWA Illumina Spleen (Nov08) RSN **" ] ], - "Striatum": [ + "Striatum mRNA": [ [ - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" + "Striatum_Exon_1212", + "HQF Striatum Affy Mouse Exon 1.0ST Gene Level (Dec09) RMA" ], [ - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" + "Striatum_Exon_0209", + "HQF Striatum Affy Mouse Exon 1.0ST Exon Level (Dec09) RMA" ], [ "UTHSC_Striatum_RankInv_1210", @@ -1416,8 +1682,12 @@ "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" ], [ - "Striatum_Exon_0209", - "HQF Striatum Exon (Feb09) RMA" + "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_ILM6.2P14RInv_1110", @@ -1428,25 +1698,29 @@ "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" ] ], - "T Cell (helper)": [ + "T Cell (helper) mRNA": [ [ "RTHC_0211_R", "HZI Thelp M430v2 (Feb11) RMA" ] ], - "T Cell (regulatory)": [ + "T Cell (regulatory) mRNA": [ [ "RTC_1106_R", "HZI Treg M430v2 (Feb11) RMA" ] ], - "Thymus": [ + "Thymus mRNA": [ [ "Illum_BXD_Thy_1108", "UWA Illumina Thymus (Nov08) RSN **" ] ], - "Ventral Tegmental Area": [ + "Ventral Tegmental Area mRNA": [ + [ + "VCUEtOH_0609_R", + "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" + ], [ "VCUSal_0609_R", "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" @@ -1454,15 +1728,17 @@ [ "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 **" ] ] }, "BXH": { - "Cartilage": [ + "Bone Femur mRNA": [ + [ + "UCLA_BXH_Femur_0113_RSN", + "UCLA GSE27483 BXH Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ] + ], + "Cartilage mRNA": [ [ "UCLA_BXHBXD_CARTILAGE_V2", "UCLA BXH and BXD Cartilage v2" @@ -1482,7 +1758,7 @@ "BXH Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "GSE16780BXH_UCLA_ML0911", "GSE16780 UCLA Mouse BXH Liver Affy HT M430A (Sep11) RMA" @@ -1495,8 +1771,22 @@ ] ] }, + "C57BL-6JxC57BL-6NJF2": { + "Genotypes": [ + [ + "C57BL-6JxC57BL-6NJF2Geno", + "C57BL-6JxC57BL-6NJF2 Genotypes" + ] + ], + "Phenotypes": [ + [ + "C57BL-6JxC57BL-6NJF2Publish", + "C57BL-6JxC57BL-6NJF2 Published Phenotypes" + ] + ] + }, "CTB6F2": { - "Adipose": [ + "Adipose mRNA": [ [ "UCLA_CTB6B6CTF2_ADIPOSE_2005", "UCLA CTB6/B6CTF2 Adipose (2005) mlratio" @@ -1510,7 +1800,7 @@ "UCLA CTB6B6CTF2 Adipose Male mlratio **" ] ], - "Brain": [ + "Brain mRNA": [ [ "UCLA_CTB6B6CTF2_BRAIN_2005", "UCLA CTB6/B6CTF2 Brain (2005) mlratio" @@ -1530,7 +1820,7 @@ "CTB6F2 Genotypes" ] ], - "Liver": [ + "Liver mRNA": [ [ "UCLA_CTB6B6CTF2_LIVER_2005", "UCLA CTB6/B6CTF2 Liver (2005) mlratio" @@ -1544,7 +1834,7 @@ "UCLA CTB6B6CTF2 Liver Male mlratio **" ] ], - "Muscle": [ + "Muscle mRNA": [ [ "UCLA_CTB6B6CTF2_MUSCLE_2005", "UCLA CTB6/B6CTF2 Muscle (2005) mlratio" @@ -1572,14 +1862,14 @@ "CXB Genotypes" ] ], - "Hippocampus": [ - [ - "HC_M2CB_1205_P", - "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" - ], + "Hippocampus mRNA": [ [ "HC_M2CB_1205_R", "Hippocampus Consortium M430v2 CXB (Dec05) RMA" + ], + [ + "HC_M2CB_1205_P", + "Hippocampus Consortium M430v2 CXB (Dec05) PDNN" ] ], "Phenotypes": [ @@ -1588,7 +1878,7 @@ "CXB Published Phenotypes" ] ], - "Spleen": [ + "Spleen mRNA": [ [ "STSPL_1107_R", "Stuart Spleen M430v2 (Nov07) RMA" @@ -1602,19 +1892,19 @@ "HS Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "OXUKHS_ILMHipp_RI0510", "OX UK HS ILM6v1.1 Hippocampus (May 2010) RankInv" ] ], - "Liver": [ + "Liver mRNA": [ [ "OXUKHS_ILMLiver_RI0510", "OX UK HS ILM6v1.1 Liver (May 2010) RankInv" ] ], - "Lung": [ + "Lung mRNA": [ [ "OXUKHS_ILMLung_RI0510", "OX UK HS ILM6v1.1 Lung (May 2010) RankInv" @@ -1640,7 +1930,7 @@ "HS-CC Published Phenotypes" ] ], - "Striatum": [ + "Striatum mRNA": [ [ "OHSU_HS-CC_ILMStr_0211", "OHSU HS-CC Striatum ILM6v1 (Feb11) RankInv" @@ -1654,7 +1944,7 @@ "LXS Genotypes" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "Illum_LXS_Hipp_loess0807", "Hippocampus Illumina (Aug07) LOESS" @@ -1684,6 +1974,14 @@ "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 (Oct08) RankInv beta" ], @@ -1694,14 +1992,6 @@ [ "Illum_LXS_Hipp_RSS_1008", "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" - ], - [ - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" ] ], "Phenotypes": [ @@ -1710,7 +2000,11 @@ "LXS Published Phenotypes" ] ], - "Prefrontal Cortex": [ + "Prefrontal Cortex mRNA": [ + [ + "VCUEtOH_0806_R", + "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" + ], [ "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" @@ -1718,31 +2012,39 @@ [ "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 **" ] ] }, "MDP": { + "Bone Femur mRNA": [ + [ + "UCLA_MDP_Femur_0113_RSN", + "UCLA GSE27483 MDP Bone Femur ILM Mouse WG-6 v1, v1.1 (Jan13) RSN" + ] + ], + "Dorsal Root Ganglia mRNA": [ + [ + "TSRI-DRG-AffyMOE430_0113-MDP", + "TSRI DRG Affy Mouse Genome 430 2.0 (Jan13) RMA MDP **" + ] + ], "Genotypes": [ [ "MDPGeno", "MDP Genotypes" ] ], - "Hippocampus": [ - [ - "HC_M2_0606_MDP", - "Hippocampus Consortium M430v2 (Jun06) RMA MDP" - ], + "Hippocampus mRNA": [ [ "UMUTAffyExon_0209_RMA_MDP", "UMUTAffy Hippocampus Exon (Feb09) RMA MDP" + ], + [ + "HC_M2_0606_MDP", + "Hippocampus Consortium M430v2 (Jun06) RMA MDP" ] ], - "Liver": [ + "Liver mRNA": [ [ "GSE16780MDP_UCLA_ML0911", "GSE16780 UCLA Mouse MDP Liver Affy HT M430A (Sep11) RMA" @@ -1758,6 +2060,10 @@ [ "JAX_CSB_L_6C_0711", "JAX Liver 6C Affy M430 2.0 (Jul11) MDP" + ], + [ + "JAX_liver_agil_MDP-0113", + "Harrill-Rusyn MDP Liver Acetaminophen Tox Study (G4121A, 2009)" ] ], "Phenotypes": [ @@ -1774,7 +2080,7 @@ "NZBXFVB-N2 Genotypes" ] ], - "Mammary Tumors": [ + "Mammary Tumors mRNA": [ [ "NCI_Mam_Tum_RMA_0409", "NCI Mammary M430v2 (Apr09) RMA" @@ -1786,11 +2092,63 @@ "NZBXFVB-N2 Published Phenotypes" ] ] + }, + "SOTNOT-OHSU": { + "Genotypes": [ + [ + "SOTNOT-OHSUGeno", + "SOTNOT-OHSU Genotypes" + ] + ], + "Phenotypes": [ + [ + "SOTNOT-OHSUPublish", + "SOTNOT-OHSU Published Phenotypes" + ] + ] + }, + "Scripps-2013": { + "Anterior Cingulate Cortex mRNA": [ + [ + "ScrBXDACC4G0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Gene Level **" + ], + [ + "ScrBXDACC4GEx0513", + "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level **" + ] + ], + "Genotypes": [ + [ + "Scripps-2013Geno", + "Scripps-2013 Genotypes" + ] + ], + "Phenotypes": [ + [ + "Scripps-2013Publish", + "Scripps-2013 Published Phenotypes" + ] + ] } }, "rat": { + "HSNIH": { + "Genotypes": [ + [ + "HSNIHGeno", + "HSNIH Genotypes" + ] + ], + "Phenotypes": [ + [ + "HSNIHPublish", + "HSNIH Published Phenotypes" + ] + ] + }, "HXBBXH": { - "Adrenal Gland": [ + "Adrenal Gland mRNA": [ [ "HXB_Adrenal_1208", "MDC/CAS/UCL Adrenal 230A (Dec08) RMA" @@ -1802,19 +2160,19 @@ "HXBBXH Genotypes" ] ], - "Heart": [ + "Heart mRNA": [ [ "HXB_Heart_1208", "MDC/CAS/UCL Heart 230_V2 (Dec08) RMA" ] ], - "Hippocampus": [ + "Hippocampus mRNA": [ [ "UT_HippRatEx_RMA_0709", "UT Hippocampus Affy RaEx 1.0 Exon (Jul09) RMA" ] ], - "Kidney": [ + "Kidney mRNA": [ [ "KI_2A_0405_M", "MDC/CAS/ICL Kidney 230A (Apr05) MAS5" @@ -1828,13 +2186,13 @@ "MDC/CAS/ICL Kidney 230A (Apr05) RMA" ] ], - "Liver": [ + "Liver mRNA": [ [ "HXB_Liver_1208", "MDC/CAS/UCL Liver 230v2 (Dec08) RMA" ] ], - "Peritoneal Fat": [ + "Peritoneal Fat mRNA": [ [ "FT_2A_0805_M", "MDC/CAS/ICL Peritoneal Fat 230A (Aug05) MAS5" @@ -1852,7 +2210,7 @@ ] }, "SRxSHRSPF2": { - "Eye": [ + "Eye mRNA": [ [ "UIOWA_Eye_RMA_0906", "UIOWA Eye mRNA RAE230v2 (Sep06) RMA" @@ -1972,6 +2330,10 @@ "Human Liver Cohort (Merck)" ], [ + "HLT", + "Human Lung Transcriptome (Rosetta/Merck)" + ], + [ "HSB", "Human Brain Transcriptome (Yale/Kavli)" ] @@ -2032,6 +2394,10 @@ "BXH" ], [ + "C57BL-6JxC57BL-6NJF2", + "C57BL/6JxC57BL/6NJ F2 Cross" + ], + [ "CTB6F2", "CastB6/B6Cast F2 UCLA" ], @@ -2058,10 +2424,22 @@ [ "NZBXFVB-N2", "NZB/FVB N2 NCI" + ], + [ + "Scripps-2013", + "Scripps C57BL/6J" + ], + [ + "SOTNOT-OHSU", + "SOTNOT-OHSU" ] ], "rat": [ [ + "HSNIH", + "NIH Heterogeneous Stock" + ], + [ "HXBBXH", "HXB/BXH" ], @@ -2177,8 +2555,8 @@ "Genotypes" ], [ - "Leaf", - "Leaf mRNA" + "Leaf mRNA", + "Leaf mRNA mRNA" ] ], "SXM": [ @@ -2191,12 +2569,12 @@ "Genotypes" ], [ - "Embryo", - "Embryo mRNA" + "Embryo mRNA", + "Embryo mRNA mRNA" ], [ - "Leaf", - "Leaf mRNA" + "Leaf mRNA", + "Leaf mRNA mRNA" ] ] }, @@ -2211,8 +2589,8 @@ "Genotypes" ], [ - "Whole Body", - "Whole Body mRNA" + "Whole Body mRNA", + "Whole Body mRNA mRNA" ] ], "Oregon-R_x_2b3": [ @@ -2225,8 +2603,8 @@ "Genotypes" ], [ - "Whole Body", - "Whole Body mRNA" + "Whole Body mRNA", + "Whole Body mRNA mRNA" ] ] }, @@ -2241,8 +2619,8 @@ "Genotypes" ], [ - "Brain", - "Brain mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ] ], "AD-cases-controls-Myers": [ @@ -2255,8 +2633,8 @@ "Genotypes" ], [ - "Brain", - "Brain mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ] ], "CANDLE": [ @@ -2269,8 +2647,12 @@ "Genotypes" ], [ - "Newborn Cord Blood", - "Newborn Cord Blood mRNA" + "Methylation", + "Methylation mRNA" + ], + [ + "Newborn Cord Blood mRNA", + "Newborn Cord Blood mRNA mRNA" ] ], "CEPH-2004": [ @@ -2283,8 +2665,8 @@ "Genotypes" ], [ - "Lymphoblast B-cell", - "Lymphoblast B-cell mRNA" + "Lymphoblast B-cell mRNA", + "Lymphoblast B-cell mRNA mRNA" ] ], "HB": [ @@ -2297,16 +2679,16 @@ "Genotypes" ], [ - "Cerebellum", - "Cerebellum mRNA" + "Cerebellum mRNA", + "Cerebellum mRNA mRNA" ], [ - "Prefrontal Cortex", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA mRNA" ], [ - "Primary Visual Cortex", - "Primary Visual Cortex mRNA" + "Primary Visual Cortex mRNA", + "Primary Visual Cortex mRNA mRNA" ] ], "HLC": [ @@ -2319,8 +2701,22 @@ "Genotypes" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" + ] + ], + "HLT": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Lung mRNA", + "Lung mRNA mRNA" ] ], "HSB": [ @@ -2333,68 +2729,68 @@ "Genotypes" ], [ - "Amygdala", - "Amygdala mRNA" + "Amygdala mRNA", + "Amygdala mRNA mRNA" ], [ - "Cerebellar Cortex", - "Cerebellar Cortex mRNA" + "Cerebellar Cortex mRNA", + "Cerebellar Cortex mRNA mRNA" ], [ - "Dorsolateral Prefrontal Cortex", - "Dorsolateral Prefrontal Cortex mRNA" + "Dorsolateral Prefrontal Cortex mRNA", + "Dorsolateral Prefrontal Cortex mRNA mRNA" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ], [ - "Inferior Temporal Cortex", - "Inferior Temporal Cortex mRNA" + "Inferior Temporal Cortex mRNA", + "Inferior Temporal Cortex mRNA mRNA" ], [ - "Medial Prefrontal Cortex", - "Medial Prefrontal Cortex mRNA" + "Medial Prefrontal Cortex mRNA", + "Medial Prefrontal Cortex mRNA mRNA" ], [ - "Mediodorsal Nucleus of Thalamus", - "Mediodorsal Nucleus of Thalamus mRNA" + "Mediodorsal Nucleus of Thalamus mRNA", + "Mediodorsal Nucleus of Thalamus mRNA mRNA" ], [ - "Orbital Prefrontal Cortex", - "Orbital Prefrontal Cortex mRNA" + "Orbital Prefrontal Cortex mRNA", + "Orbital Prefrontal Cortex mRNA mRNA" ], [ - "Posterior Inferior Parietal Cortex", - "Posterior Inferior Parietal Cortex mRNA" + "Posterior Inferior Parietal Cortex mRNA", + "Posterior Inferior Parietal Cortex mRNA mRNA" ], [ - "Posterior Superior Temporal Cortex", - "Posterior Superior Temporal Cortex mRNA" + "Posterior Superior Temporal Cortex mRNA", + "Posterior Superior Temporal Cortex mRNA mRNA" ], [ - "Primary Auditory (A1) Cortex", - "Primary Auditory (A1) Cortex mRNA" + "Primary Auditory (A1) Cortex mRNA", + "Primary Auditory (A1) Cortex mRNA mRNA" ], [ - "Primary Motor (M1) Cortex", - "Primary Motor (M1) Cortex mRNA" + "Primary Motor (M1) Cortex mRNA", + "Primary Motor (M1) Cortex mRNA mRNA" ], [ - "Primary Somatosensory (S1) Cortex", - "Primary Somatosensory (S1) Cortex mRNA" + "Primary Somatosensory (S1) Cortex mRNA", + "Primary Somatosensory (S1) Cortex mRNA mRNA" ], [ - "Primary Visual Cortex", - "Primary Visual Cortex mRNA" + "Primary Visual Cortex mRNA", + "Primary Visual Cortex mRNA mRNA" ], [ - "Striatum", - "Striatum mRNA" + "Striatum mRNA", + "Striatum mRNA mRNA" ], [ - "Ventrolateral Prefrontal Cortex", - "Ventrolateral Prefrontal Cortex mRNA" + "Ventrolateral Prefrontal Cortex mRNA", + "Ventrolateral Prefrontal Cortex mRNA mRNA" ] ] }, @@ -2409,24 +2805,24 @@ "Genotypes" ], [ - "Amygdala", - "Amygdala mRNA" + "Amygdala mRNA", + "Amygdala mRNA mRNA" ], [ - "Brain", - "Brain mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ], [ - "Nucleus Accumbens", - "Nucleus Accumbens mRNA" + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA mRNA" ], [ - "Prefrontal Cortex", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA mRNA" ] ] }, @@ -2441,8 +2837,8 @@ "Genotypes" ], [ - "Mammary Tumors", - "Mammary Tumors mRNA" + "Mammary Tumors mRNA", + "Mammary Tumors mRNA mRNA" ] ], "AXBXA": [ @@ -2455,12 +2851,20 @@ "Genotypes" ], [ - "Eye", - "Eye mRNA" + "Bone Femur mRNA", + "Bone Femur mRNA mRNA" + ], + [ + "Eye mRNA", + "Eye mRNA mRNA" + ], + [ + "Heart mRNA", + "Heart mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ] ], "B6BTBRF2": [ @@ -2473,8 +2877,8 @@ "Genotypes" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ] ], "B6D2F2": [ @@ -2487,8 +2891,8 @@ "Genotypes" ], [ - "Brain", - "Brain mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ] ], "B6D2F2-PSU": [ @@ -2501,8 +2905,8 @@ "Genotypes" ], [ - "Muscle", - "Muscle mRNA" + "Muscle mRNA", + "Muscle mRNA mRNA" ] ], "B6D2RI": [ @@ -2515,8 +2919,8 @@ "Genotypes" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ] ], "BDF2-1999": [ @@ -2529,8 +2933,8 @@ "Genotypes" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ] ], "BDF2-2005": [ @@ -2543,8 +2947,8 @@ "Genotypes" ], [ - "Striatum", - "Striatum mRNA" + "Striatum mRNA", + "Striatum mRNA mRNA" ] ], "BHF2": [ @@ -2557,20 +2961,20 @@ "Genotypes" ], [ - "Adipose", - "Adipose mRNA" + "Adipose mRNA", + "Adipose mRNA mRNA" ], [ - "Brain", - "Brain mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ], [ - "Muscle", - "Muscle mRNA" + "Muscle mRNA", + "Muscle mRNA mRNA" ] ], "BHHBF2": [ @@ -2583,20 +2987,20 @@ "Genotypes" ], [ - "Adipose", - "Adipose mRNA" + "Adipose mRNA", + "Adipose mRNA mRNA" ], [ - "Brain", - "Brain mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ], [ - "Muscle", - "Muscle mRNA" + "Muscle mRNA", + "Muscle mRNA mRNA" ] ], "BXD": [ @@ -2609,112 +3013,120 @@ "Genotypes" ], [ - "Adrenal Gland", - "Adrenal Gland mRNA" + "Adrenal Gland mRNA", + "Adrenal Gland mRNA mRNA" + ], + [ + "Amygdala mRNA", + "Amygdala mRNA mRNA" + ], + [ + "Bone Femur mRNA", + "Bone Femur mRNA mRNA" ], [ - "Amygdala", - "Amygdala mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ], [ - "Brain", - "Brain mRNA" + "Cartilage mRNA", + "Cartilage mRNA mRNA" ], [ - "Cartilage", - "Cartilage mRNA" + "Cerebellum mRNA", + "Cerebellum mRNA mRNA" ], [ - "Cerebellum", - "Cerebellum mRNA" + "Eye mRNA", + "Eye mRNA mRNA" ], [ - "Eye", - "Eye mRNA" + "Hematopoietic Cells mRNA", + "Hematopoietic Cells mRNA mRNA" ], [ - "Hematopoietic Cells", - "Hematopoietic Cells mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hypothalamus mRNA", + "Hypothalamus mRNA mRNA" ], [ - "Hypothalamus", - "Hypothalamus mRNA" + "Kidney mRNA", + "Kidney mRNA mRNA" ], [ - "Kidney", - "Kidney mRNA" + "Leucocytes mRNA", + "Leucocytes mRNA mRNA" ], [ - "Leucocytes", - "Leucocytes mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Liver Proteome", + "Liver Proteome mRNA" ], [ - "Lung", - "Lung mRNA" + "Lung mRNA", + "Lung mRNA mRNA" ], [ - "Midbrain", - "Midbrain mRNA" + "Midbrain mRNA", + "Midbrain mRNA mRNA" ], [ - "Muscle", - "Muscle mRNA" + "Muscle mRNA", + "Muscle mRNA mRNA" ], [ - "Neocortex", - "Neocortex mRNA" + "Neocortex mRNA", + "Neocortex mRNA mRNA" ], [ - "Nucleus Accumbens", - "Nucleus Accumbens mRNA" + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA mRNA" ], [ - "Pituitary Gland", - "Pituitary Gland mRNA" + "Pituitary Gland mRNA", + "Pituitary Gland mRNA mRNA" ], [ - "Popliteal Lymph Node", - "Popliteal Lymph Node mRNA" + "Popliteal Lymph Node mRNA", + "Popliteal Lymph Node mRNA mRNA" ], [ - "Prefrontal Cortex", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA mRNA" ], [ - "Retina", - "Retina mRNA" + "Retina mRNA", + "Retina mRNA mRNA" ], [ - "Spleen", - "Spleen mRNA" + "Spleen mRNA", + "Spleen mRNA mRNA" ], [ - "Striatum", - "Striatum mRNA" + "Striatum mRNA", + "Striatum mRNA mRNA" ], [ - "T Cell (helper)", - "T Cell (helper) mRNA" + "T Cell (helper) mRNA", + "T Cell (helper) mRNA mRNA" ], [ - "T Cell (regulatory)", - "T Cell (regulatory) mRNA" + "T Cell (regulatory) mRNA", + "T Cell (regulatory) mRNA mRNA" ], [ - "Thymus", - "Thymus mRNA" + "Thymus mRNA", + "Thymus mRNA mRNA" ], [ - "Ventral Tegmental Area", - "Ventral Tegmental Area mRNA" + "Ventral Tegmental Area mRNA", + "Ventral Tegmental Area mRNA mRNA" ] ], "BXH": [ @@ -2727,12 +3139,26 @@ "Genotypes" ], [ - "Cartilage", - "Cartilage mRNA" + "Bone Femur mRNA", + "Bone Femur mRNA mRNA" + ], + [ + "Cartilage mRNA", + "Cartilage mRNA mRNA" + ], + [ + "Liver mRNA", + "Liver mRNA mRNA" + ] + ], + "C57BL-6JxC57BL-6NJF2": [ + [ + "Phenotypes", + "Phenotypes" ], [ - "Liver", - "Liver mRNA" + "Genotypes", + "Genotypes" ] ], "CTB6F2": [ @@ -2745,20 +3171,20 @@ "Genotypes" ], [ - "Adipose", - "Adipose mRNA" + "Adipose mRNA", + "Adipose mRNA mRNA" ], [ - "Brain", - "Brain mRNA" + "Brain mRNA", + "Brain mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ], [ - "Muscle", - "Muscle mRNA" + "Muscle mRNA", + "Muscle mRNA mRNA" ] ], "CXB": [ @@ -2771,12 +3197,12 @@ "Genotypes" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ], [ - "Spleen", - "Spleen mRNA" + "Spleen mRNA", + "Spleen mRNA mRNA" ] ], "HS": [ @@ -2789,16 +3215,16 @@ "Genotypes" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ], [ - "Lung", - "Lung mRNA" + "Lung mRNA", + "Lung mRNA mRNA" ] ], "HS-CC": [ @@ -2811,8 +3237,8 @@ "Genotypes" ], [ - "Striatum", - "Striatum mRNA" + "Striatum mRNA", + "Striatum mRNA mRNA" ] ], "LXS": [ @@ -2825,12 +3251,12 @@ "Genotypes" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ], [ - "Prefrontal Cortex", - "Prefrontal Cortex mRNA" + "Prefrontal Cortex mRNA", + "Prefrontal Cortex mRNA mRNA" ] ], "MDP": [ @@ -2843,12 +3269,20 @@ "Genotypes" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Bone Femur mRNA", + "Bone Femur mRNA mRNA" + ], + [ + "Dorsal Root Ganglia mRNA", + "Dorsal Root Ganglia mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" + ], + [ + "Liver mRNA", + "Liver mRNA mRNA" ] ], "NZBXFVB-N2": [ @@ -2861,12 +3295,46 @@ "Genotypes" ], [ - "Mammary Tumors", - "Mammary Tumors mRNA" + "Mammary Tumors mRNA", + "Mammary Tumors mRNA mRNA" + ] + ], + "SOTNOT-OHSU": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], + "Scripps-2013": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ], + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA mRNA" ] ] }, "rat": { + "HSNIH": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "Genotypes", + "Genotypes" + ] + ], "HXBBXH": [ [ "Phenotypes", @@ -2877,28 +3345,28 @@ "Genotypes" ], [ - "Adrenal Gland", - "Adrenal Gland mRNA" + "Adrenal Gland mRNA", + "Adrenal Gland mRNA mRNA" ], [ - "Heart", - "Heart mRNA" + "Heart mRNA", + "Heart mRNA mRNA" ], [ - "Hippocampus", - "Hippocampus mRNA" + "Hippocampus mRNA", + "Hippocampus mRNA mRNA" ], [ - "Kidney", - "Kidney mRNA" + "Kidney mRNA", + "Kidney mRNA mRNA" ], [ - "Liver", - "Liver mRNA" + "Liver mRNA", + "Liver mRNA mRNA" ], [ - "Peritoneal Fat", - "Peritoneal Fat mRNA" + "Peritoneal Fat mRNA", + "Peritoneal Fat mRNA mRNA" ] ], "SRxSHRSPF2": [ @@ -2911,8 +3379,8 @@ "Genotypes" ], [ - "Eye", - "Eye mRNA" + "Eye mRNA", + "Eye mRNA mRNA" ] ] }, |