diff options
| author | zsloan | 2016-02-18 17:14:26 +0000 |
|---|---|---|
| committer | zsloan | 2016-02-18 17:14:26 +0000 |
| commit | 6d8503e53b48ba2e398ff7950d2a722ffc2b6026 (patch) | |
| tree | 0805a4a77b464a2575519cdda466522b0f9ab14b | |
| parent | 7f5536635ac20f7c670e4dc8e650f27d47503d78 (diff) | |
| download | genenetwork2-6d8503e53b48ba2e398ff7950d2a722ffc2b6026.tar.gz | |
Edited gen_select_dataset to remove confidential datasets
Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential
| -rwxr-xr-x | wqflask/maintenance/gen_select_dataset.py | 27 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 1542 |
2 files changed, 901 insertions, 668 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index ea0d4a56..e080050e 100755 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -76,7 +76,7 @@ def parse_db_uri(db_uri): def get_species(): """Build species list""" - Cursor.execute("select Name, MenuName from Species order by OrderId") + Cursor.execute("select Name, MenuName from Species where Species.Name != 'macaque monkey' order by OrderId") species = list(Cursor.fetchall()) return species @@ -90,8 +90,8 @@ def get_groups(species): ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and (PublishFreeze.InbredSetId = InbredSet.Id - or GenoFreeze.InbredSetId = InbredSet.Id - or ProbeFreeze.InbredSetId = InbredSet.Id) + or GenoFreeze.InbredSetId = InbredSet.Id + or ProbeFreeze.InbredSetId = InbredSet.Id) group by InbredSet.Name order by InbredSet.Name""", (species_name)) groups[species_name] = list(Cursor.fetchall()) @@ -169,7 +169,9 @@ def build_types(species, group): results = [] for result in Cursor.fetchall(): if len(result): - results.append((result[0], result[0])) + these_datasets = build_datasets(species, group, result[0]) + if len(these_datasets) > 0: + results.append((result[0], result[0])) return results @@ -182,7 +184,10 @@ def get_datasets(types): #print("type_list: ", type_list) datasets[species][group] = {} for type_name in type_list: - datasets[species][group][type_name[0]] = build_datasets(species, group, type_name[0]) + these_datasets = build_datasets(species, group, type_name[0]) + if len(these_datasets) > 0: + datasets[species][group][type_name[0]] = these_datasets + return datasets @@ -195,7 +200,8 @@ def build_datasets(species, group, type_name): InbredSet.Name = %s and PublishFreeze.InbredSetId = InbredSet.Id and InfoFiles.InfoPageName = PublishFreeze.Name and - PublishFreeze.public > 0 order by + PublishFreeze.public > 0 and + PublishFreeze.confidentiality < 1 order by PublishFreeze.CreateTime desc""", (group)) results = Cursor.fetchone() @@ -214,7 +220,8 @@ def build_datasets(species, group, type_name): InbredSet.Name = %s and GenoFreeze.InbredSetId = InbredSet.Id and InfoFiles.InfoPageName = GenoFreeze.ShortName and - GenoFreeze.public > 0 order by + GenoFreeze.public > 0 and + GenoFreeze.confidentiality < 1 order by GenoFreeze.CreateTime desc""", (group)) results = Cursor.fetchone() @@ -232,9 +239,9 @@ def build_datasets(species, group, type_name): ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where Species.Name = %s and Species.Id = InbredSet.SpeciesId and InbredSet.Name = %s and - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s - and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = - InbredSet.Id and ProbeSetFreeze.public > 0 order by + ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s and + ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and + ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 order by ProbeSetFreeze.CreateTime desc""", (species, group, type_name)) dataset_results = Cursor.fetchall() diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 5194cb96..2154541c 100755 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -210,6 +210,13 @@ "AD-cases-controls-MyersGeno", "AD-cases-controls-Myers Genotypes" ] + ], + "Phenotypes": [ + [ + "None", + "AD-cases-controls-MyersPublish", + "AD-cases-controls-Myers Published Phenotypes" + ] ] }, "Aging-Brain-UCI": { @@ -227,6 +234,13 @@ "GSE11882 UCI Human Hippocampus Affy U133 Plus2 (Sep13) RMA" ] ], + "Phenotypes": [ + [ + "None", + "Aging-Brain-UCIPublish", + "Aging-Brain-UCI Published Phenotypes" + ] + ], "Postcentral Gyrus mRNA": [ [ "462", @@ -273,18 +287,6 @@ ] }, "CANDLE": { - "Methylation": [ - [ - "423", - "CANDLE_Meth27_0313", - "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) **" - ], - [ - "422", - "CANDLE_Meth_0313", - "CANDLE Newborn Cord ILM HumanMethylation27 (Mar13) Z-Score **" - ] - ], "Newborn Cord Blood mRNA": [ [ "324", @@ -880,6 +882,379 @@ ] ] }, + "GTEx_v5": { + "Adrenal Gland mRNA": [ + [ + "720", + "GTEXv5_AdrGla_0915", + "GTEXv5 Human Adrenal Gland RefSeq (Sep15) RPKM log2" + ] + ], + "Amygdala mRNA": [ + [ + "725", + "GTEXv5_Amy_0915", + "GTEXv5 Human Brain Amygdala RefSeq (Sep15) RPKM log2" + ] + ], + "Anterior Cingulate Cortex mRNA": [ + [ + "726", + "GTEXv5_AntCtx_0915", + "GTEXv5 Human Brain Anterior Cingulate Cortex BA24 RefSeq (Sep15) RPKM log2" + ] + ], + "Aorta mRNA": [ + [ + "721", + "GTEXv5_ArtAor_0915", + "GTEXv5 Human Artery Aorta RefSeq (Sep15) RPKM log2" + ] + ], + "Bladder mRNA": [ + [ + "724", + "GTEXv5_Bla_0915", + "GTEXv5 Human Bladder RefSeq (Sep15) RPKM log2" + ] + ], + "Bone Marrow mRNA": [ + [ + "740", + "GTEXv5_BM_0915", + "GTEXv5 Human Cells-Leukemia Cell Line CML RefSeq (Sep15) RPKM log2" + ] + ], + "Breast - Mammary Tissue mRNA": [ + [ + "738", + "GTEXv5_BrMa_0915", + "GTEXv5 Human Breast Mammary Tissue RefSeq (Sep15) RPKM log2" + ] + ], + "Caudate mRNA": [ + [ + "727", + "GTEXv5_BrCa_0915", + "GTEXv5 Human Brain Caudate Basal Ganglia RefSeq (Sep15) RPKM log2" + ] + ], + "Cells - EBV-Transformed Lymphocytes mRNA": [ + [ + "739", + "GTEXv5_EBV_0915", + "GTEXv5 Human Cells-EBV-Transformed Lymphocytes RefSeq (Sep15) RPKM log2" + ] + ], + "Cells - Transformed Fibroblasts mRNA": [ + [ + "741", + "GTEXv5_CTF_0915", + "GTEXv5 Human Cells-Transformed Fibroblasts RefSeq (Sep15) RPKM log2" + ] + ], + "Cerebellar Cortex mRNA": [ + [ + "730", + "GTEXv5_BrCtx_0915", + "GTEXv5 Human Brain Cortex RefSeq (Sep15) RPKM log2" + ] + ], + "Cerebellar Hemisphere mRNA": [ + [ + "728", + "GTEXv5_CerH_0915", + "GTEXv5 Human Brain Cerebellar Hemisphere RefSeq (Sep15) RPKM log2" + ] + ], + "Cerebellum mRNA": [ + [ + "729", + "GTEXv5_BrCe_0915", + "GTEXv5 Human Brain Cerebellum RefSeq (Sep15) RPKM log2" + ] + ], + "Cervix mRNA": [ + [ + "742", + "GTEXv5_CerEct_0915", + "GTEXv5 Human Cervix-Ectocervix RefSeq (Sep15) RPKM log2" + ] + ], + "Colon - Sigmoid mRNA": [ + [ + "743", + "GTEXv5_ColSig_0915", + "GTEXv5 Human Colon-Sigmoid RefSeq (Sep15) RPKM log2" + ] + ], + "Colon - Transverse mRNA": [ + [ + "744", + "GTEXv5_ColTra_0915", + "GTEXv5 Human Colon-Transverse RefSeq (Sep15) RPKM log2" + ] + ], + "Coronary mRNA": [ + [ + "722", + "GTEXv5_ArtCor_0915", + "GTEXv5 Human Artery Coronary RefSeq (Sep15) RPKM log2" + ] + ], + "Esophagus - Gastroesophageal mRNA": [ + [ + "745", + "GTEXv5_GastJun_0915", + "GTEXv5 Human Esophagus - Gastroesophageal Junction RefSeq (Sep15) RPKM log2" + ] + ], + "Esophagus - Mucosa mRNA": [ + [ + "746", + "GTEXv5_EsoMu_0915", + "GTEXv5 Human Esophagus - Mucosa RefSeq (Sep15) RPKM log2" + ] + ], + "Esophagus - Muscularis mRNA": [ + [ + "747", + "GTEXv5_EsoMus_0915", + "GTEXv5 Human Esophagus - Muscularis RefSeq (Sep15) RPKM log2" + ] + ], + "Fallopian Tube mRNA": [ + [ + "748", + "GTEXv5_Fatu_0915", + "GTEXv5 Human Fallopian Tube RefSeq (Sep15) RPKM log2" + ] + ], + "Frontal Cortex mRNA": [ + [ + "731", + "GTEXv5_BrFr_0915", + "GTEXv5 Human Brain Frontal Cortex BA9 RefSeq (Sep15) RPKM log2" + ] + ], + "Heart - Atrial Appendage mRNA": [ + [ + "749", + "GTEXv5_HAA_0915", + "GTEXv5 Human Heart - Atrial Appendage RefSeq (Sep15) RPKM log2" + ] + ], + "Heart - Left Ventricle mRNA": [ + [ + "750", + "GTEXv5_LV_0915", + "GTEXv5 Human Heart - Left Ventricle RefSeq (Sep15) RPKM log2" + ] + ], + "Hippocampus mRNA": [ + [ + "732", + "GTEXv5_Hip_0915", + "GTEXv5 Human Brain Hippocampus RefSeq (Sep15) RPKM log2" + ] + ], + "Hypothalamus mRNA": [ + [ + "733", + "GTEXv5_Hiptha_0915", + "GTEXv5 Human Brain Hypothalamus RefSeq (Sep15) RPKM log2" + ] + ], + "Kidney mRNA": [ + [ + "751", + "GTEXv5_Kidn_0915", + "GTEXv5 Human Kidney - Cortex RefSeq (Sep15) RPKM log2" + ] + ], + "Liver mRNA": [ + [ + "752", + "GTEXv5_Liv_0915", + "GTEXv5 Human Liver RefSeq (Sep15) RPKM log2" + ] + ], + "Lung mRNA": [ + [ + "753", + "GTEXv5_Lung_0915", + "GTEXv5 Human Lung RefSeq (Sep15) RPKM log2" + ] + ], + "Muscle mRNA": [ + [ + "754", + "GTEXv5_MuSk_0915", + "GTEXv5 Human Muscle - Skeletal RefSeq (Sep15) RPKM log2" + ] + ], + "Nerve - Tibial mRNA": [ + [ + "755", + "GTEXv5_Tib_0915", + "GTEXv5 Human Nerve - Tibial RefSeq (Sep15) RPKM log2" + ] + ], + "Nucleus Accumbens mRNA": [ + [ + "734", + "GTEXv5_NuAcc_0915", + "GTEXv5 Human Brain Nucleus Accumbens Basal Ganglia RefSeq (Sep15) RPKM log2" + ] + ], + "Ovary mRNA": [ + [ + "756", + "GTEXv5_Ov_0915", + "GTEXv5 Human Ovary RefSeq (Sep15) RPKM log2" + ] + ], + "Pancreas mRNA": [ + [ + "757", + "GTEXv5_Panc_0915", + "GTEXv5 Human Pancreas RefSeq (Sep15) RPKM log2" + ] + ], + "Pituitary Gland mRNA": [ + [ + "758", + "GTEXv5_Pit_0915", + "GTEXv5 Human Pituitary RefSeq (Sep15) RPKM log2" + ] + ], + "Prostate mRNA": [ + [ + "759", + "GTEXv5_Prost_0915", + "GTEXv5 Human Prostate RefSeq (Sep15) RPKM log2" + ] + ], + "Putamen mRNA": [ + [ + "735", + "GTEXv5_PutB_0915", + "GTEXv5 Human Brain Putamen Basal Ganglia RefSeq (Sep15) RPKM log2" + ] + ], + "Salivary Gland mRNA": [ + [ + "760", + "GTEXv5_SalGl_0915", + "GTEXv5 Human Salivary Gland Minor RefSeq (Sep15) RPKM log2" + ] + ], + "Skin - Not Sun Exposed (Suprapubic) mRNA": [ + [ + "761", + "GTEXv5_SkN_0915", + "GTEXv5 Human Skin-Not Sun Exposed-Suprapubic RefSeq (Sep15) RPKM log2" + ] + ], + "Skin - Sun Exposed (Lower leg) mRNA": [ + [ + "762", + "GTEXv5_SkS_0915", + "GTEXv5 Human Skin-Sun Exposed-Lower Leg RefSeq (Sep15) RPKM log2" + ] + ], + "Small Intestine - Terminal Ileum mRNA": [ + [ + "763", + "GTEXv5_SInt_0915", + "GTEXv5 Human Small Intestine - Terminal Ileum RefSeq (Sep15) RPKM log2" + ] + ], + "Spinal Cord mRNA": [ + [ + "736", + "GTEXv5_SpCo_0915", + "GTEXv5 Human Brain Spinal Cord Cervical C-1 RefSeq (Sep15) RPKM log2" + ] + ], + "Spleen mRNA": [ + [ + "764", + "GTEXv5_Sple_0915", + "GTEXv5 Human Spleen RefSeq (Sep15) RPKM log2" + ] + ], + "Stomach mRNA": [ + [ + "765", + "GTEXv5_Sto_0915", + "GTEXv5 Human Stomach RefSeq (Sep15) RPKM log2" + ] + ], + "Subcutaneous mRNA": [ + [ + "718", + "GTEXv5_AdipSub_0915", + "GTEXv5 Human Adipose Subcutaneous RefSeq (Sep15) RPKM log2" + ] + ], + "Substantia Nigra mRNA": [ + [ + "737", + "GTEXv5_SubN_0915", + "GTEXv5 Human Brain Substantia Nigra RefSeq (Sep15) RPKM log2" + ] + ], + "Testis mRNA": [ + [ + "766", + "GTEXv5_Test_0915", + "GTEXv5 Human Testis RefSeq (Sep15) RPKM log2" + ] + ], + "Thyroid mRNA": [ + [ + "767", + "GTEXv5_Thy_0915", + "GTEXv5 Human Thyroid RefSeq (Sep15) RPKM log2" + ] + ], + "Tibial mRNA": [ + [ + "723", + "GTEXv5_ArtTib_0915", + "GTEXv5 Human Artery Tibial RefSeq (Sep15) RPKM log2" + ] + ], + "Uterus mRNA": [ + [ + "768", + "GTEXv5_Ut_0915", + "GTEXv5 Human Uterus RefSeq (Sep15) RPKM log2" + ] + ], + "Vagina mRNA": [ + [ + "769", + "GTEXv5_Vag_0915", + "GTEXv5 Human Vagina RefSeq (Sep15) RPKM log2" + ] + ], + "Visceral mRNA": [ + [ + "719", + "GTEXv5_AdiVis_0915", + "GTEXv5 Human Adipose Visceral Omentum RefSeq (Sep15) RPKM log2" + ] + ], + "Whole Blood mRNA": [ + [ + "770", + "GTEXv5_Wbl_0915", + "GTEXv5 Human Whole Blood RefSeq (Sep15) RPKM log2" + ] + ] + }, "HB": { "Cerebellum mRNA": [ [ @@ -991,16 +1366,6 @@ "Super Series GSE23546 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" ], [ - "452", - "luCA_GSE23352HLT0613", - "UL/GSE23352 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA (Jun11) RMA" - ], - [ - "453", - "UBC-GSE23529HLT0613", - "UBC/GSE23529 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" - ], - [ "454", "GRNG-GSE23545HLT0613", "GRNG/GSE23545 Whole-Genome GXD Non-Tumorous Human Lung Tissues Affy HuRSTA array (Jun11) RMA" @@ -1064,6 +1429,13 @@ "Human Orbital Prefrontal Cortex Affy Hu-Exon 1.0 ST (Jul11) Quantile" ] ], + "Phenotypes": [ + [ + "None", + "HSBPublish", + "HSB Published Phenotypes" + ] + ], "Posterior Inferior Parietal Cortex mRNA": [ [ "338", @@ -1122,45 +1494,6 @@ ] } }, - "macaque monkey": { - "Macaca-fasicularis": { - "Amygdala mRNA": [ - [ - "255", - "INIA_MacFas_AMG_RMA_0110", - "INIA Macaca fasicularis Amygdala (Jan10) RMA **" - ] - ], - "Brain mRNA": [ - [ - "251", - "INIA_MacFas_brain_RMA_0110", - "INIA Macaca fasicularis Brain (Jan10) RMA **" - ] - ], - "Hippocampus mRNA": [ - [ - "254", - "INIA_MacFas_Hc_RMA_0110", - "INIA Macaca fasicularis Hippocampus (Jan10) RMA **" - ] - ], - "Nucleus Accumbens mRNA": [ - [ - "253", - "INIA_MacFas_Ac_RMA_0110", - "INIA Macaca fasicularis Nucleus Accumbens (Jan10) RMA **" - ] - ], - "Prefrontal Cortex mRNA": [ - [ - "252", - "INIA_MacFas_Pf_RMA_0110", - "INIA Macaca fasicularis Prefrontal Cortex (Jan10) RMA **" - ] - ] - } - }, "mouse": { "AKXD": { "Genotypes": [ @@ -1263,11 +1596,6 @@ "B6D2F2": { "Brain mRNA": [ [ - "77", - "BRF2_M_0805_R", - "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" - ], - [ "76", "BRF2_M_0805_M", "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5" @@ -1278,6 +1606,11 @@ "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN" ], [ + "77", + "BRF2_M_0805_R", + "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA" + ], + [ "33", "BRF2_M_0304_P", "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN" @@ -1309,35 +1642,20 @@ "B6D2F2-PSU Genotypes" ] ], - "Muscle mRNA": [ - [ - "134", - "PSU-B6D2F2_0812", - "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA **" - ], - [ - "404", - "PSU-B6D2F2_F0812", - "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Females **" - ], - [ - "405", - "PSU-B6D2F2_M0812", - "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males **" - ], + "Phenotypes": [ [ - "406", - "PSU-B6D2F2_M2000812", - "PSU B6D2F2 Muscle Affy Mouse Genome 430 2.0 (Aug12) RMA Males Aged 200 **" + "None", + "B6D2F2-PSUPublish", + "B6D2F2-PSU Published Phenotypes" ] ] }, "B6D2RI": { - "Hippocampus mRNA": [ + "Phenotypes": [ [ - "391", - "UTHSC_B6D2RI_H_0912", - "UTHSC B6D2RI Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA **" + "None", + "B6D2RIPublish", + "B6D2RI Published Phenotypes" ] ] }, @@ -1442,21 +1760,11 @@ "UCLA BHF2 Liver (June05) mlratio" ] ], - "Muscle mRNA": [ - [ - "202", - "UCLA_BHF2_MUSCLE_MALE", - "UCLA BHF2 Muscle Male mlratio **" - ], - [ - "203", - "UCLA_BHF2_MUSCLE_FEMALE", - "UCLA BHF2 Muscle Female mlratio **" - ], + "Phenotypes": [ [ - "168", - "UCLA_BHF2_MUSCLE_0605", - "UCLA BHF2 Muscle (June05) mlratio **" + "None", + "BHF2Publish", + "BHF2 Published Phenotypes" ] ] }, @@ -1609,35 +1917,10 @@ "414", "UCLA_BXD-on_Femur_0113_RSN", "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v2.0 (Jan13) RSN" - ], - [ - "464", - "UTHSCWGU88BFMG1013", - "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA **" - ], - [ - "465", - "UTHSCWGU88BFMEx1013", - "UTHSC WGU88 Male Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA **" - ], - [ - "466", - "UTHSCWGU88BFFG1013", - "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Gene Level (Oct13) RMA **" - ], - [ - "467", - "UTHSCWGU88BFFEx1013", - "UTHSC WGU88 Female Bone Femur AFFY Mouse Gene ST 2.0 Exon Level (Oct13) RMA **" ] ], "Brain mRNA": [ [ - "589", - "UTHSC_BXD_WB_RNASeqtrim1112", - "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed 2.0" - ], - [ "164", "UTHSC_BXD_WB_RNASeq1112", "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed" @@ -1720,76 +2003,6 @@ "9", "CB_M_1003_M", "SJUT Cerebellum mRNA M430 (Oct03) MAS5" - ], - [ - "436", - "CMMTUBCBXDCerILM0513", - "UBC/CMMT BXD Cerebellum All Ages Combined ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "441", - "CMMTUBCBXDG12CerILM0513", - "UBC/CMMT BXD E12 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "442", - "CMMTUBCBXDG15CerILM0513", - "UBC/CMMT BXD E15 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "443", - "CMMTUBCBXDG18CerILM0513", - "UBC/CMMT BXD E18 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "437", - "CMMTUBCBXDP00CerILM0513", - "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "438", - "CMMTUBCBXDP03CerILM0513", - "UBC/CMMT BXD P3 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "439", - "CMMTUBCBXDP06CerILM0513", - "UBC/CMMT BXD P6 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "440", - "CMMTUBCBXDP09CerILM0513", - "UBC/CMMT BXD P9 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv **" - ], - [ - "415", - "GenEx_BXD_CerebEt_RMA_0213", - "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes **" - ], - [ - "416", - "GenEx_BXD_CerebEt_RMA_F_0213", - "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Females **" - ], - [ - "417", - "GenEx_BXD_CerebEt_RMA_M_0213", - "GenEx BXD EtOH Cerebellum Affy M430 2.0 (Feb13) RMA Males **" - ], - [ - "418", - "GenEx_BXD_CerebSal_RMA_0213", - "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Both Sexes **" - ], - [ - "419", - "GenEx_BXD_CerebSal_RMA_F_0213", - "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Females **" - ], - [ - "420", - "GenEx_BXD_CerebSal_RMA_M_0213", - "GenEx BXD Sal Cerebellum Affy M430 2.0 (Feb13) RMA Males **" ] ], "Eye mRNA": [ @@ -1801,32 +2014,32 @@ [ "10", "gn10", - "Eye M430v2 No Mutant/Mutant (Aug12) RMA **" + "Eye M430v2 No Mutant/Mutant (Aug12) RMA" ], [ "261", "Eye_M2_0908_R_NB", - "Eye M430v2 Mutant Gpnmb (Sep08) RMA **" + "Eye M430v2 Mutant Gpnmb (Sep08) RMA" ], [ "262", "Eye_M2_0908_R_ND", - "Eye M430v2 WT Gpnmb (Sep08) RMA **" - ], - [ - "279", - "Eye_M2_0908_R_WT", - "Eye M430v2 WT Tyrp1 (Sep08) RMA **" + "Eye M430v2 WT Gpnmb (Sep08) RMA" ], [ "278", "Eye_M2_0908_R_MT", - "Eye M430v2 Mutant Tyrp1 (Sep08) RMA **" + "Eye M430v2 Mutant Tyrp1 (Sep08) RMA" ], [ "382", "Eye_M2_0908_WTWT", - "Eye M430v2 WT WT (Sep08) RMA **" + "Eye M430v2 WT WT (Sep08) RMA" + ], + [ + "279", + "Eye_M2_0908_R_WT", + "Eye M430v2 WT Tyrp1 (Sep08) RMA" ], [ "400", @@ -1839,11 +2052,33 @@ "Howell et al. 2011, DBA/2J Glaucoma Retina M430 2.0 (Sep11) RMA" ] ], + "Fecal Metabolome": [ + [ + "717", + "RTI_RCMRC-BXDFecMetlog0814", + "RTI RCMRC BXD Fecal Metabolites CD+HFD (Aug14) Log2" + ], + [ + "716", + "RTI_RCMRC-BXDFecMetHFlog0814", + "RTI RCMRC BXD Fecal Metabolites HFD (Aug14) Log2" + ], + [ + "715", + "RTI_RCMRC-BXDFecMetLFlog0814", + "RTI RCMRC BXD Fecal Metabolites CD (Aug14) Log2" + ] + ], "Gastrointestinal mRNA": [ [ "539", "UTHSC_GutGL_0414", - "UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene Level (Apr14) RMA **" + "UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene Level (Apr14) RMA" + ], + [ + "597", + "UTHSC_GutExL_0414", + "UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Exon Level (Apr14) RMA" ] ], "Genotypes": [ @@ -1853,28 +2088,6 @@ "BXD Genotypes" ] ], - "Heart mRNA": [ - [ - "485", - "EPFL-LISPBXDHeCD0114", - "EPFL/LISP BXD CD Heart Affy Mouse Gene 2.0 ST Gene Level (Jan14) RMA **" - ], - [ - "486", - "EPFL-LISPBXDHeHFD0114", - "EPFL/LISP BXD HFD Heart Affy Mouse Gene 2.0 ST Gene Level (Jan14) RMA **" - ], - [ - "487", - "EPFL-LISPBXDHeCDEx0114", - "EPFL/LISP BXD CD Heart Affy Mouse Gene 2.0 ST Exon Level (Jan14) RMA **" - ], - [ - "488", - "EPFL-LISPBXDHeHFDEx0114", - "EPFL/LISP BXD HFD Heart Affy Mouse Gene 2.0 ST Exon Level (Jan14) RMA **" - ] - ], "Hematopoietic Cells mRNA": [ [ "149", @@ -1922,6 +2135,13 @@ "GNF Stem Cells U74Av2 (Mar04) RMA" ] ], + "Hippocampal Precursor Cells mRNA": [ + [ + "706", + "CRTD_HipPreCell1214", + "CRTD BXD Hippocampal Precursor Cells ILM MouseWG-6_R13 (Dec14) Quantile" + ] + ], "Hippocampus mRNA": [ [ "112", @@ -1939,6 +2159,11 @@ "Hippocampus Consortium M430v2 (Jun06) RMA" ], [ + "206", + "UMUTAffyExon_0209_RMA", + "UMUTAffy Hippocampus Exon (Feb09) RMA" + ], + [ "291", "UT_ILM_BXD_hipp_5T_1112", "UTHSC Hippocampus Illumina v6.1 All Combined (Nov12) RankInv" @@ -1969,11 +2194,6 @@ "UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv" ], [ - "206", - "UMUTAffyExon_0209_RMA", - "UMUTAffy Hippocampus Exon (Feb09) RMA" - ], - [ "242", "UT_ILM_BXD_hipp_NON_0909", "UTHSC Hippocampus Illumina v6.1 NON (Sep09) RankInv" @@ -1997,23 +2217,6 @@ "245", "UT_ILM_BXD_hipp_RSE_0909", "UTHSC Hippocampus Illumina v6.1 RSE (Sep09) RankInv" - ], - [ - "393", - "UTHSC_BXD_HArev3_0912", - "UTHSC BXD Aged Hippocampus rev3 Affy Mouse Gene 1.0 ST (Sep12) RMA **" - ], - [ - "392", - "UTHSC_BXD_H_0912", - "UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Sep12) RMA Exon Level **" - ] - ], - "Hippocampus microRNA": [ - [ - "491", - "UTHSC_BXD_Hip_miRNASeq0214", - "UTHSC BXD Hippocampus Ion Torrent microRNA (Feb14) RPKM **" ] ], "Hypothalamus mRNA": [ @@ -2060,16 +2263,16 @@ ], "Kidney mRNA": [ [ - "239", - "MA_M2F_0706_R", - "Mouse kidney M430v2 Female (Aug06) RMA" - ], - [ "240", "MA_M2M_0706_R", "Mouse kidney M430v2 Male (Aug06) RMA" ], [ + "239", + "MA_M2F_0706_R", + "Mouse kidney M430v2 Female (Aug06) RMA" + ], + [ "118", "MA_M2_0806_R", "Mouse kidney M430v2 Sex Balanced (Aug06) RMA" @@ -2090,49 +2293,82 @@ "Mouse Kidney M430v2 (Jul06) RMA" ] ], - "Leucocytes mRNA": [ - [ - "218", - "Illum_BXD_PBL_1108", - "UWA Illumina PBL (Nov08) RSN **" - ] - ], "Liver Metabolome": [ [ + "473", + "EPFL-LISP_LivPMetCDHFD1213", + "EPFL/LISP BXD Liver Polar Metabolites CD+HFD (Jun14)" + ], + [ "474", "EPFL-LISP_LivPMetHFD1213", - "EPFL/LISP BXD Liver Polar Metabolites HFD (Jun14) **" + "EPFL/LISP BXD Liver Polar Metabolites HFD (Jun14)" ], [ "475", "EPFL-LISP_LivPMetCD1213", - "EPFL/LISP BXD Liver Polar Metabolites CD (Jun14) **" + "EPFL/LISP BXD Liver Polar Metabolites CD (Jun14)" + ], + [ + "713", + "EPFL-LISP_LivPMetlog2HFD1213", + "EPFL/LISP BXD Liver Polar Metabolites HFD (Jun14) Log2" + ], + [ + "714", + "EPFL-LISP_LivPMetlog2CD1213", + "EPFL/LISP BXD Liver Polar Metabolites CD (Jun14) Log2" ] ], "Liver Proteome": [ [ - "541", - "EPFLETHZBXDprotHFD0514", - "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (May14) SWATH **" + "704", + "EPFLETHZBXDprotCD_LS1114", + "EPFL/ETHZ BXD Liver, Chow Diet (Oct14) Light SWATH" ], [ - "540", - "EPFLETHZBXDprotCD0514", - "EPFL/ETHZ BXD Liver, Soluble Proteins CD (May14) SWATH **" + "705", + "EPFLETHZBXDprotHF_LS1114", + "EPFL/ETHZ BXD Liver, High Fat Diet (Oct14) Light SWATH" ], [ - "489", - "EPFLBXDprotHFDRPN0214", - "EPFL/LISP BXD Liver, Soluble Proteins HFD (Feb14) SRM **" + "703", + "EPFLBXDprotCD-CDHFDRPN0214", + "EPFL/LISP BXD Liver, Soluble Proteins CD+HFD (Feb14) SRM" ], [ "490", "EPFLBXDprotCDRPN0214", - "EPFL/LISP BXD Liver, Soluble Proteins CD (Feb14) SRM **" + "EPFL/LISP BXD Liver, Soluble Proteins CD (Feb14) SRM" + ], + [ + "489", + "EPFLBXDprotHFDRPN0214", + "EPFL/LISP BXD Liver, Soluble Proteins HFD (Feb14) SRM" + ], + [ + "540", + "EPFLETHZBXDprotCD0514", + "EPFL/ETHZ BXD Liver, Soluble Proteins CD (Jun14) SWATH" + ], + [ + "541", + "EPFLETHZBXDprotHFD0514", + "EPFL/ETHZ BXD Liver, Soluble Proteins HFD (Jun14) SWATH" ] ], "Liver mRNA": [ [ + "700", + "UT-VGX_HGL1014", + "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA" + ], + [ + "701", + "UT-VGX_HEL1014", + "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Exon Level (Oct14) RMA" + ], + [ "373", "GSE16780_UCLA_ML0911", "GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA" @@ -2143,6 +2379,11 @@ "SUH BXD Liver CCl4-treated Affy Mouse Gene 1.0 ST (Jun11) RMA" ], [ + "702", + "SUH_Liv_RMAEx_0611", + "SUH BXD Liver CCl4-treated Affy Mouse Gene 1.0 ST Exon Level (Jun11) RMA" + ], + [ "430", "EPFLMouseLiverRMA0413", "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" @@ -2156,56 +2397,6 @@ "432", "EPFLMouseLiverCDRMA0413", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" - ], - [ - "433", - "EPFLMouseLiverBothExRMA0413", - "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level **" - ], - [ - "256", - "GenEx_BXD_liverEt_M5_0912", - "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Both Sexes **" - ], - [ - "257", - "GenEx_BXD_liverEt_M5M_0912", - "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Males **" - ], - [ - "258", - "GenEx_BXD_liverEt_M5F_0912", - "GenEx BXD EtOH Liver Affy M430 2.0 (Sep12) MAS5 Females **" - ], - [ - "307", - "GenEx_BXD_liverEt_RMA_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "308", - "GenEx_BXD_liverEt_RMA_M_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "309", - "GenEx_BXD_liverEt_RMA_F_0211", - "GenEx BXD EtOH Liver Affy M430 2.0 (Feb11) RMA Females **" - ], - [ - "310", - "GenEx_BXD_liverSal_RMA_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Both Sexes **" - ], - [ - "311", - "GenEx_BXD_liverSal_RMA_M_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Males **" - ], - [ - "312", - "GenEx_BXD_liverSal_RMA_F_0211", - "GenEx BXD Sal Liver Affy M430 2.0 (Feb11) RMA Females **" ] ], "Lung mRNA": [ @@ -2218,21 +2409,6 @@ "161", "HZI_0408_M", "HZI Lung M430v2 (Apr08) MAS5" - ], - [ - "468", - "HZI_PR8M-F_1113", - "HZI PR8M-Infected Lungs Females RNAseq (Nov13) RPKM **" - ], - [ - "387", - "HZI_PR8M_Q_0612", - "HZI PR8M-Infected Lungs Agilent4x44 (Apr12) Quantile Females **" - ], - [ - "424", - "HZI_LTCF_0313", - "HZI Lung Time Course Flu PR8M (Mar13) Schughart **" ] ], "Midbrain mRNA": [ @@ -2242,18 +2418,6 @@ "VU BXD Midbrain Agilent SurePrint G3 Mouse GE (May12) Quantile" ] ], - "Muscle Metabolome": [ - [ - "477", - "EPFL-LISP_MusPMetHFD1213", - "EPFL/LISP BXD Muscle Polar Metabolites HFD (Jun14) **" - ], - [ - "478", - "EPFL-LISP_MusPMetCD1213", - "EPFL/LISP BXD Muscle Polar Metabolites CD (Jun14) **" - ] - ], "Muscle mRNA": [ [ "395", @@ -2328,31 +2492,6 @@ "156", "VCUSalo_1007_R", "VCU BXD NAc Sal M430 2.0 (Oct07) RMA" - ], - [ - "155", - "VCUEtOH_1007_R", - "VCU BXD NAc EtOH M430 2.0 (Oct07) RMA **" - ], - [ - "154", - "VCUSal_1007_R", - "VCU BXD NAc EtOH vs Sal M430 2.0 (Oct07) Sscore **" - ], - [ - "409", - "VCU_NAc_Air_0113_R", - "VCU BXD NAc CIE Air M430 2.0 (Jan13) RMA **" - ], - [ - "408", - "VCU_NAc_Et_0113_R", - "VCU BXD NAc CIE EtOH M430 2.0 (Jan13) RMA **" - ], - [ - "407", - "VCU_NAc_AvE_0113_Ss", - "VCU BXD NAc EtOH vs CIE Air M430 2.0 (Jan13) Sscore **" ] ], "Phenotypes": [ @@ -2384,13 +2523,6 @@ "INIA Pituitary Affy MoGene 1.0ST (Jun12) RMA Exon Level" ] ], - "Popliteal Lymph Node mRNA": [ - [ - "390", - "STJ_PLN_0912", - "St Jude BXD Popliteal Lymph Node Affy HT MG-430 PM (Sep12) RMA **" - ] - ], "Prefrontal Cortex mRNA": [ [ "135", @@ -2406,33 +2538,18 @@ "137", "VCUSal_1006_R", "VCU BXD PFC Et vs Sal M430 2.0 (Dec06) Sscore" - ], - [ - "299", - "VCU_PF_AvE_0111_Ss", - "VCU BXD PFC EtOH vs CIE Air M430 2.0 (Jan11) Sscore **" - ], - [ - "300", - "VCU_PF_Et_0111_R", - "VCU BXD PFC CIE EtOH M430 2.0 (Jan11) RMA **" - ], - [ - "301", - "VCU_PF_Air_0111_R", - "VCU BXD PFC CIE Air M430 2.0 (Jan11) RMA **" ] ], "Retina mRNA": [ [ - "302", - "G2NEI_ILM_Retina_BXD_RI0410", - "Normal HEI Retina (April 2010) RankInv" + "709", + "DoDCMMRPRetMoGene2_0515", + "DoD CDMRP Retina Affy MoGene 2.0 ST (May15) RMA Gene Level" ], [ - "267", - "Illum_Retina_BXD_RankInv0410", - "Full HEI Retina (April 2010) RankInv" + "710", + "DoDCMMRPRetMoGene2Ex_0515", + "DoD CDMRP Retina Affy MoGene 2.0 ST (May15) RMA Exon Level" ], [ "385", @@ -2440,49 +2557,14 @@ "ONC HEI Retina (April 2012) RankInv" ], [ - "471", - "DoDTATRCRetMoGene2_1313", - "DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA" - ], - [ - "472", - "DoDTATRCRetExMoGene2_1313", - "DoD TATRC Retina Affy MoGene 2.0 ST (Dec13) RMA Exon Level" - ], - [ - "434", - "ONCRetMoGene2_0413", - "DoD TATRC Retina Affy MoGene 2.0 ST (Oct13) RMA **" - ], - [ - "435", - "ONCRetExMoGene2_0413", - "DoD TATRC Retina Affy MoGene 2.0 ST (Oct13) RMA Exon Level **" - ], - [ - "479", - "DoDTATRCRetBLMoGene2_1213", - "DoD TATRC Retina Blast Affy MoGene 2.0 ST (Dec13) RMA **" - ], - [ - "480", - "DoDTATRCRetBLExMoGene2_1213", - "DoD TATRC Retina Blast Affy MoGene 2.0 ST (Dec13) RMA Exon Level **" - ], - [ - "386", - "B6D2ONCILM_0412", - "B6D2 ONC Retina (April 2012) RankInv **" - ], - [ - "371", - "HEIONCvsCRetILM6_0911", - "HEI ONC vs Control Retina Illumina V6.2 (Sep11) RankInv **" + "302", + "G2NEI_ILM_Retina_BXD_RI0410", + "Normal HEI Retina (April 2010) RankInv" ], [ - "372", - "G2HEIONCRetILM6_0911", - "G2 HEI ONC Retina Illumina V6.2 (Sep11) RankInv **" + "267", + "Illum_Retina_BXD_RankInv0410", + "Full HEI Retina (April 2010) RankInv" ] ], "Spleen mRNA": [ @@ -2492,6 +2574,16 @@ "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA" ], [ + "773", + "UTHSC_SPLs1_RMA_1210", + "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Set1" + ], + [ + "774", + "UTHSC_SPLs2_RMA_1210", + "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Set2" + ], + [ "286", "UTHSC_SPL_RMA_1210M", "UTHSC Affy MoGene 1.0 ST Spleen (Dec10) RMA Males" @@ -2520,15 +2612,20 @@ "227", "IoP_SPL_RMA_0509", "IoP Affy MOE 430v2 Spleen (May09) RMA" - ], - [ - "216", - "Illum_BXD_Spl_1108", - "UWA Illumina Spleen (Nov08) RSN **" ] ], "Striatum mRNA": [ [ + "376", + "DevStriatum_ILM6.2P3RInv_1111", + "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv" + ], + [ + "377", + "DevStriatum_ILM6.2P14RInv_1111", + "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv" + ], + [ "399", "Striatum_Exon_1212", "HQF Striatum Affy Mouse Exon 1.0ST Gene Level (Dec09) RMA" @@ -2577,26 +2674,6 @@ "66", "SA_M2_0405_RR", "HBP Rosen Striatum M430V2 (Apr05) RMA Orig" - ], - [ - "376", - "DevStriatum_ILM6.2P3RInv_1111", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov11) RankInv **" - ], - [ - "377", - "DevStriatum_ILM6.2P14RInv_1111", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov11) RankInv **" - ], - [ - "277", - "DevStriatum_ILM6.2P14RInv_1110", - "BIDMC/UTHSC Dev Striatum P14 ILMv6.2 (Nov10) RankInv **" - ], - [ - "276", - "DevStriatum_ILM6.2P3RInv_1110", - "BIDMC/UTHSC Dev Striatum P3 ILMv6.2 (Nov10) RankInv **" ] ], "T Cell (helper) mRNA": [ @@ -2612,30 +2689,6 @@ "RTC_1106_R", "HZI Treg M430v2 (Feb11) RMA" ] - ], - "Thymus mRNA": [ - [ - "217", - "Illum_BXD_Thy_1108", - "UWA Illumina Thymus (Nov08) RSN **" - ] - ], - "Ventral Tegmental Area mRNA": [ - [ - "229", - "VCUEtOH_0609_R", - "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **" - ], - [ - "228", - "VCUSal_0609_R", - "VCU BXD VTA Sal M430 2.0 (Jun09) RMA **" - ], - [ - "230", - "VCUEtvsSal_0609_R", - "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) Sscore **" - ] ] }, "BXH": { @@ -2701,22 +2754,47 @@ ] ] }, + "CIE-INIA": { + "LCM Brain Regions mRNA": [ + [ + "776", + "INIA_LCM_CAB_1215", + "INIA LCM (11 Regions) CIE/AIR/BAS RNA-seq Transcript Level (Dec15)" + ], + [ + "772", + "INIA_LCM_1215", + "INIA LCM (11 Regions) CIE/AIR RNA-seq Transcript Level (Dec15)" + ], + [ + "775", + "INIA_LCMB_1215", + "INIA LCM (11 Regions) BASELINE RNA-seq Transcript Level (Dec15)" + ] + ], + "Phenotypes": [ + [ + "None", + "CIE-INIAPublish", + "CIE-INIA Published Phenotypes" + ] + ] + }, + "CMS": { + "Phenotypes": [ + [ + "None", + "CMSPublish", + "CMS Published Phenotypes" + ] + ] + }, "CTB6F2": { "Adipose mRNA": [ [ "170", "UCLA_CTB6B6CTF2_ADIPOSE_2005", "UCLA CTB6/B6CTF2 Adipose (2005) mlratio" - ], - [ - "189", - "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE", - "UCLA CTB6B6CTF2 Adipose Female mlratio **" - ], - [ - "188", - "UCLA_CTB6B6CTF2_ADIPOSE_MALE", - "UCLA CTB6B6CTF2 Adipose Male mlratio **" ] ], "Brain mRNA": [ @@ -2748,16 +2826,6 @@ "172", "UCLA_CTB6B6CTF2_LIVER_2005", "UCLA CTB6/B6CTF2 Liver (2005) mlratio" - ], - [ - "193", - "UCLA_CTB6B6CTF2_LIVER_FEMALE", - "UCLA CTB6B6CTF2 Liver Female mlratio **" - ], - [ - "192", - "UCLA_CTB6B6CTF2_LIVER_MALE", - "UCLA CTB6B6CTF2 Liver Male mlratio **" ] ], "Muscle mRNA": [ @@ -2765,16 +2833,6 @@ "173", "UCLA_CTB6B6CTF2_MUSCLE_2005", "UCLA CTB6/B6CTF2 Muscle (2005) mlratio" - ], - [ - "195", - "UCLA_CTB6B6CTF2_MUSCLE_FEMALE", - "UCLA CTB6B6CTF2 Muscle Female mlratio **" - ], - [ - "194", - "UCLA_CTB6B6CTF2_MUSCLE_MALE", - "UCLA CTB6B6CTF2 Muscle Male mlratio **" ] ], "Phenotypes": [ @@ -2869,6 +2927,31 @@ ], "Hippocampus mRNA": [ [ + "219", + "Illum_LXS_Hipp_NON_1008", + "Hippocampus Illumina NON (Oct08) RankInv beta" + ], + [ + "212", + "Illum_LXS_Hipp_RSE_1008", + "Hippocampus Illumina RSE (Oct08) RankInv beta" + ], + [ + "214", + "Illum_LXS_Hipp_NOE_1008", + "Hippocampus Illumina NOE (Oct08) RankInv beta" + ], + [ + "211", + "Illum_LXS_Hipp_RSS_1008", + "Hippocampus Illumina RSS (Oct08) RankInv beta" + ], + [ + "213", + "Illum_LXS_Hipp_NOS_1008", + "Hippocampus Illumina NOS (Oct08) RankInv beta" + ], + [ "143", "Illum_LXS_Hipp_loess0807", "Hippocampus Illumina (Aug07) LOESS" @@ -2902,31 +2985,6 @@ "133", "Hipp_Illumina_RankInv_0507", "Hippocampus Illumina (May07) RankInv" - ], - [ - "219", - "Illum_LXS_Hipp_NON_1008", - "Hippocampus Illumina NON (Oct08) RankInv beta" - ], - [ - "212", - "Illum_LXS_Hipp_RSE_1008", - "Hippocampus Illumina RSE (Oct08) RankInv beta" - ], - [ - "214", - "Illum_LXS_Hipp_NOE_1008", - "Hippocampus Illumina NOE (Oct08) RankInv beta" - ], - [ - "211", - "Illum_LXS_Hipp_RSS_1008", - "Hippocampus Illumina RSS (Oct08) RankInv beta" - ], - [ - "213", - "Illum_LXS_Hipp_NOS_1008", - "Hippocampus Illumina NOS (Oct08) RankInv beta" ] ], "Phenotypes": [ @@ -2938,19 +2996,9 @@ ], "Prefrontal Cortex mRNA": [ [ - "131", - "VCUEtOH_0806_R", - "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **" - ], - [ "130", "VCUSal_0806_R", "VCU LXS PFC Sal M430A 2.0 (Aug06) RMA" - ], - [ - "132", - "VCUEt_vs_Sal_0806_R", - "VCU LXS PFC Et vs Sal M430A 2.0 (Aug06) Sscore **" ] ] }, @@ -3064,20 +3112,7 @@ ] ] }, - "Scripps-2013": { - "Anterior Cingulate Cortex mRNA": [ - [ - "450", - "ScrBXDACC4G0513", - "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Gene Level **" - ], - [ - "451", - "ScrBXDACC4GEx0513", - "Scripps BXD ACC 4 Groups Affy Mouse Gene 1.0 ST (May13) RMA Exon Level **" - ] - ] - } + "Scripps-2013": {} }, "rat": { "HSNIH": { @@ -3279,7 +3314,11 @@ ], [ "GTEx", - "All Tissues, RNA-Seq GTEx v3" + "GTEx v3 All Tissues, RNA-Seq" + ], + [ + "GTEx_v5", + "GTEx v5 All Tissues, RNA-Seq" ], [ "HB", @@ -3302,12 +3341,6 @@ "Brain, Development: Normal Gene Expression (Yale/Sestan)" ] ], - "macaque monkey": [ - [ - "Macaca-fasicularis", - "Macaca fasicularis (Cynomolgus monkey)" - ] - ], "mouse": [ [ "AKXD", @@ -3331,7 +3364,7 @@ ], [ "B6D2RI", - "B6D2RI Aged" + "BXD Aged" ], [ "BDF2-1999", @@ -3362,6 +3395,14 @@ "Reduced Complexity Cross (B6JxB6N F2)" ], [ + "CIE-INIA", + "Chronic Intermittent Ethanol" + ], + [ + "CMS", + "Chronic Mild Stress" + ], + [ "CTB6F2", "CastB6/B6Cast F2 UCLA" ], @@ -3439,10 +3480,6 @@ "Human" ], [ - "macaque monkey", - "Macaque monkey" - ], - [ "mouse", "Mouse" ], @@ -3565,6 +3602,10 @@ ], "AD-cases-controls-Myers": [ [ + "Phenotypes", + "Phenotypes" + ], + [ "Genotypes", "Genotypes" ], @@ -3575,6 +3616,10 @@ ], "Aging-Brain-UCI": [ [ + "Phenotypes", + "Phenotypes" + ], + [ "Entorhinal Cortex mRNA", "Entorhinal Cortex mRNA" ], @@ -3615,10 +3660,6 @@ "Phenotypes" ], [ - "Methylation", - "Methylation" - ], - [ "Newborn Cord Blood mRNA", "Newborn Cord Blood mRNA" ] @@ -3819,6 +3860,220 @@ "Whole Blood mRNA" ] ], + "GTEx_v5": [ + [ + "Adrenal Gland mRNA", + "Adrenal Gland mRNA" + ], + [ + "Amygdala mRNA", + "Amygdala mRNA" + ], + [ + "Anterior Cingulate Cortex mRNA", + "Anterior Cingulate Cortex mRNA" + ], + [ + "Aorta mRNA", + "Aorta mRNA" + ], + [ + "Bladder mRNA", + "Bladder mRNA" + ], + [ + "Bone Marrow mRNA", + "Bone Marrow mRNA" + ], + [ + "Breast - Mammary Tissue mRNA", + "Breast - Mammary Tissue mRNA" + ], + [ + "Caudate mRNA", + "Caudate mRNA" + ], + [ + "Cells - EBV-Transformed Lymphocytes mRNA", + "Cells - EBV-Transformed Lymphocytes mRNA" + ], + [ + "Cells - Transformed Fibroblasts mRNA", + "Cells - Transformed Fibroblasts mRNA" + ], + [ + "Cerebellar Cortex mRNA", + "Cerebellar Cortex mRNA" + ], + [ + "Cerebellar Hemisphere mRNA", + "Cerebellar Hemisphere mRNA" + ], + [ + "Cerebellum mRNA", + "Cerebellum mRNA" + ], + [ + "Cervix mRNA", + "Cervix mRNA" + ], + [ + "Colon - Sigmoid mRNA", + "Colon - Sigmoid mRNA" + ], + [ + "Colon - Transverse mRNA", + "Colon - Transverse mRNA" + ], + [ + "Coronary mRNA", + "Coronary mRNA" + ], + [ + "Esophagus - Gastroesophageal mRNA", + "Esophagus - Gastroesophageal mRNA" + ], + [ + "Esophagus - Mucosa mRNA", + "Esophagus - Mucosa mRNA" + ], + [ + "Esophagus - Muscularis mRNA", + "Esophagus - Muscularis mRNA" + ], + [ + "Fallopian Tube mRNA", + "Fallopian Tube mRNA" + ], + [ + "Frontal Cortex mRNA", + "Frontal Cortex mRNA" + ], + [ + "Heart - Atrial Appendage mRNA", + "Heart - Atrial Appendage mRNA" + ], + [ + "Heart - Left Ventricle mRNA", + "Heart - Left Ventricle mRNA" + ], + [ + "Hippocampus mRNA", + "Hippocampus mRNA" + ], + [ + "Hypothalamus mRNA", + "Hypothalamus mRNA" + ], + [ + "Kidney mRNA", + "Kidney mRNA" + ], + [ + "Liver mRNA", + "Liver mRNA" + ], + [ + "Lung mRNA", + "Lung mRNA" + ], + [ + "Muscle mRNA", + "Muscle mRNA" + ], + [ + "Nerve - Tibial mRNA", + "Nerve - Tibial mRNA" + ], + [ + "Nucleus Accumbens mRNA", + "Nucleus Accumbens mRNA" + ], + [ + "Ovary mRNA", + "Ovary mRNA" + ], + [ + "Pancreas mRNA", + "Pancreas mRNA" + ], + [ + "Pituitary Gland mRNA", + "Pituitary Gland mRNA" + ], + [ + "Prostate mRNA", + "Prostate mRNA" + ], + [ + "Putamen mRNA", + "Putamen mRNA" + ], + [ + "Salivary Gland mRNA", + "Salivary Gland mRNA" + ], + [ + "Skin - Not Sun Exposed (Suprapubic) mRNA", + "Skin - Not Sun Exposed (Suprapubic) mRNA" + ], + [ + "Skin - Sun Exposed (Lower leg) mRNA", + "Skin - Sun Exposed (Lower leg) mRNA" + ], + [ + "Small Intestine - Terminal Ileum mRNA", + "Small Intestine - Terminal Ileum mRNA" + ], + [ + "Spinal Cord mRNA", + "Spinal Cord mRNA" + ], + [ + "Spleen mRNA", + "Spleen mRNA" + ], + [ + "Stomach mRNA", + "Stomach mRNA" + ], + [ + "Subcutaneous mRNA", + "Subcutaneous mRNA" + ], + [ + "Substantia Nigra mRNA", + "Substantia Nigra mRNA" + ], + [ + "Testis mRNA", + "Testis mRNA" + ], + [ + "Thyroid mRNA", + "Thyroid mRNA" + ], + [ + "Tibial mRNA", + "Tibial mRNA" + ], + [ + "Uterus mRNA", + "Uterus mRNA" + ], + [ + "Vagina mRNA", + "Vagina mRNA" + ], + [ + "Visceral mRNA", + "Visceral mRNA" + ], + [ + "Whole Blood mRNA", + "Whole Blood mRNA" + ] + ], "HB": [ [ "Cerebellum mRNA", @@ -3857,6 +4112,10 @@ ], "HSB": [ [ + "Phenotypes", + "Phenotypes" + ], + [ "Amygdala mRNA", "Amygdala mRNA" ], @@ -3922,30 +4181,6 @@ ] ] }, - "macaque monkey": { - "Macaca-fasicularis": [ - [ - "Amygdala mRNA", - "Amygdala mRNA" - ], - [ - "Brain mRNA", - "Brain mRNA" - ], - [ - "Hippocampus mRNA", - "Hippocampus mRNA" - ], - [ - "Nucleus Accumbens mRNA", - "Nucleus Accumbens mRNA" - ], - [ - "Prefrontal Cortex mRNA", - "Prefrontal Cortex mRNA" - ] - ] - }, "mouse": { "AKXD": [ [ @@ -4009,18 +4244,18 @@ ], "B6D2F2-PSU": [ [ - "Genotypes", - "Genotypes" + "Phenotypes", + "Phenotypes" ], [ - "Muscle mRNA", - "Muscle mRNA" + "Genotypes", + "Genotypes" ] ], "B6D2RI": [ [ - "Hippocampus mRNA", - "Hippocampus mRNA" + "Phenotypes", + "Phenotypes" ] ], "BDF2-1999": [ @@ -4045,6 +4280,10 @@ ], "BHF2": [ [ + "Phenotypes", + "Phenotypes" + ], + [ "Genotypes", "Genotypes" ], @@ -4059,10 +4298,6 @@ [ "Liver mRNA", "Liver mRNA" - ], - [ - "Muscle mRNA", - "Muscle mRNA" ] ], "BHHBF2": [ @@ -4129,20 +4364,20 @@ "Eye mRNA" ], [ - "Gastrointestinal mRNA", - "Gastrointestinal mRNA" + "Fecal Metabolome", + "Fecal Metabolome" ], [ - "Heart mRNA", - "Heart mRNA" + "Gastrointestinal mRNA", + "Gastrointestinal mRNA" ], [ "Hematopoietic Cells mRNA", "Hematopoietic Cells mRNA" ], [ - "Hippocampus microRNA", - "Hippocampus microRNA" + "Hippocampal Precursor Cells mRNA", + "Hippocampal Precursor Cells mRNA" ], [ "Hippocampus mRNA", @@ -4157,10 +4392,6 @@ "Kidney mRNA" ], [ - "Leucocytes mRNA", - "Leucocytes mRNA" - ], - [ "Liver Metabolome", "Liver Metabolome" ], @@ -4181,10 +4412,6 @@ "Midbrain mRNA" ], [ - "Muscle Metabolome", - "Muscle Metabolome" - ], - [ "Muscle mRNA", "Muscle mRNA" ], @@ -4201,10 +4428,6 @@ "Pituitary Gland mRNA" ], [ - "Popliteal Lymph Node mRNA", - "Popliteal Lymph Node mRNA" - ], - [ "Prefrontal Cortex mRNA", "Prefrontal Cortex mRNA" ], @@ -4227,14 +4450,6 @@ [ "T Cell (regulatory) mRNA", "T Cell (regulatory) mRNA" - ], - [ - "Thymus mRNA", - "Thymus mRNA" - ], - [ - "Ventral Tegmental Area mRNA", - "Ventral Tegmental Area mRNA" ] ], "BXH": [ @@ -4269,6 +4484,22 @@ "Genotypes" ] ], + "CIE-INIA": [ + [ + "Phenotypes", + "Phenotypes" + ], + [ + "LCM Brain Regions mRNA", + "LCM Brain Regions mRNA" + ] + ], + "CMS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "CTB6F2": [ [ "Phenotypes", @@ -4407,12 +4638,7 @@ "Genotypes" ] ], - "Scripps-2013": [ - [ - "Anterior Cingulate Cortex mRNA", - "Anterior Cingulate Cortex mRNA" - ] - ] + "Scripps-2013": [] }, "rat": { "HSNIH": [ |