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-rwxr-xr-xwqflask/base/webqtlConfig.py3
-rwxr-xr-xwqflask/base/webqtlConfigLocal.py20
-rw-r--r--wqflask/maintenance/gen_select_dataset.py55
l---------wqflask/maintenance/our_settings.py1
-rw-r--r--wqflask/secure_server.py3
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json1330
6 files changed, 943 insertions, 469 deletions
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"
]
]
},
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 20:24:29 +0000