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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:extrahepatic cholestasis
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Accession:DOID:13619 term browser browse the term
Definition:Impairment of bile flow in the large BILE DUCTS by mechanical obstruction or stricture due to benign or malignant processes.
Synonyms:exact_synonym: Bile Duct Obstruction, Extrahepatic;   Extrahepatic Biliary Stasis;   extrahepatic obstructive biliary disease
 primary_id: MESH:D001651;   RDO:0004994
 xref: NCI:C34420
For additional species annotation, visit the Alliance of Genome Resources.


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extrahepatic cholestasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ABCA1 ATP binding cassette subfamily A member 1 ISO mRNA,protein:increased expression:liver, basolateral plasma membrane (rat) RGD PMID:28660384 RGD:21203516 NCBI chr 9:104,781,006...104,928,232
Ensembl chr 9:104,781,006...104,928,155
JBrowse link
G ABCC4 ATP binding cassette subfamily C member 4 treatment ISO mRNA:increased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr13:95,019,835...95,301,451
Ensembl chr13:95,019,835...95,301,475
JBrowse link
G ACTA2 actin alpha 2, smooth muscle EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:88,935,074...88,991,397
Ensembl chr10:88,935,074...88,991,339
JBrowse link
G ALB albumin EXP CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 4:73,404,287...73,421,482
Ensembl chr 4:73,397,114...73,421,482
JBrowse link
G CCN2 cellular communication network factor 2 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 6:131,948,176...131,951,372
Ensembl chr 6:131,948,176...131,951,372
JBrowse link
G CD68 CD68 molecule EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr17:7,579,638...7,582,111
Ensembl chr17:7,579,491...7,582,111
JBrowse link
G COL1A1 collagen type I alpha 1 chain EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr17:50,184,096...50,201,649
Ensembl chr17:50,183,289...50,201,632
Ensembl chr17:50,183,289...50,201,632
JBrowse link
G COL3A1 collagen type III alpha 1 chain EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 2:188,974,373...189,012,746
Ensembl chr 2:188,974,373...189,012,746
Ensembl chr 2:188,974,373...189,012,746
JBrowse link
G CRH corticotropin releasing hormone ISO protein:decreased expression:hypothalamus (rat) RGD PMID:8387536 RGD:5490980 NCBI chr 8:66,176,376...66,178,464
Ensembl chr 8:66,176,376...66,178,464
JBrowse link
G CYGB cytoglobin EXP CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr17:76,527,356...76,557,692
Ensembl chr17:76,527,356...76,551,175
JBrowse link
G CYP27A1 cytochrome P450 family 27 subfamily A member 1 treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr 2:218,781,733...218,815,293
Ensembl chr 2:218,781,749...218,815,293
JBrowse link
G CYP7A1 cytochrome P450 family 7 subfamily A member 1 treatment ISO mRNA:decreased expression:liver (rat)
mRNA:decreased expression:liver, nucleus (rat)
RGD PMID:29360226, PMID:28660384 RGD:14995480, RGD:21203516 NCBI chr 8:58,490,178...58,500,163
Ensembl chr 8:58,490,178...58,500,163
JBrowse link
G CYP8B1 cytochrome P450 family 8 subfamily B member 1 treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr 3:42,872,192...42,875,879
Ensembl chr 3:42,856,005...42,875,898
JBrowse link
G FOS Fos proto-oncogene, AP-1 transcription factor subunit EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr14:75,278,828...75,282,230
Ensembl chr14:75,278,826...75,282,230
JBrowse link
G GJB1 gap junction protein beta 1 ISO mRNA,protein:decreased expression:liver: RGD PMID:7762611 RGD:7349397 NCBI chr  X:71,215,239...71,225,516
Ensembl chr  X:71,212,811...71,225,516
Ensembl chr  X:71,212,811...71,225,516
JBrowse link
G GJB2 gap junction protein beta 2 ISO RGD PMID:7762611 RGD:7349397 NCBI chr13:20,187,470...20,192,938
Ensembl chr13:20,187,463...20,192,938
JBrowse link
G HAMP hepcidin antimicrobial peptide ISO mRNA:decreased expression:liver RGD PMID:19652645 RGD:11041639 NCBI chr19:35,282,528...35,285,143
Ensembl chr19:35,280,716...35,285,143
JBrowse link
G HMGB1 high mobility group box 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr13:30,456,704...30,617,597
Ensembl chr13:30,456,704...30,617,597
JBrowse link
G HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 ISO mRNA, protein:decreased expression:liver, mitochondrion (rat) RGD PMID:12399220 RGD:2326121 NCBI chr 1:119,747,996...119,768,932
Ensembl chr 1:119,748,002...119,768,905
Ensembl chr 1:119,748,002...119,768,905
JBrowse link
G HNF1A HNF1 homeobox A ISO mRNA,protein,DNA:decreased expression, decreased binding, decreased expression:liver, nuclear (rat) RGD PMID:15723437 RGD:14700989 NCBI chr12:120,977,683...121,002,512
Ensembl chr12:120,978,543...121,002,512
JBrowse link
G IL1B interleukin 1 beta EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 2:112,829,751...112,836,843
Ensembl chr 2:112,829,751...112,836,816
JBrowse link
G IL6 interleukin 6 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 7:22,725,889...22,732,002
Ensembl chr 7:22,725,884...22,732,002
JBrowse link
G JUN Jun proto-oncogene, AP-1 transcription factor subunit EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 1:58,780,791...58,784,047
Ensembl chr 1:58,780,791...58,784,047
JBrowse link
G KEAP1 kelch like ECH associated protein 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr19:10,486,125...10,503,356
Ensembl chr19:10,486,125...10,503,558
JBrowse link
G LGALS1 galectin 1 ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr22:37,675,636...37,679,802
Ensembl chr22:37,675,636...37,679,802
JBrowse link
G MAP3K7 mitogen-activated protein kinase kinase kinase 7 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 6:90,513,579...90,587,072
Ensembl chr 6:90,513,573...90,587,072
JBrowse link
G MAPK1 mitogen-activated protein kinase 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr22:21,759,657...21,867,680
Ensembl chr22:21,754,500...21,867,680
Ensembl chr22:21,754,500...21,867,680
JBrowse link
G MAPK14 mitogen-activated protein kinase 14 EXP CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 6:36,027,711...36,122,964
Ensembl chr 6:36,027,677...36,111,236
JBrowse link
G MAPK3 mitogen-activated protein kinase 3 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr16:30,114,105...30,123,309
Ensembl chr16:30,114,105...30,123,506
JBrowse link
G MAPK8 mitogen-activated protein kinase 8 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:48,306,673...48,439,360
Ensembl chr10:48,306,639...48,439,360
JBrowse link
G MAPK9 mitogen-activated protein kinase 9 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:180,233,143...180,292,083
Ensembl chr 5:180,233,143...180,292,099
JBrowse link
G MMP2 matrix metallopeptidase 2 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr16:55,478,830...55,506,691
Ensembl chr16:55,389,700...55,506,691
JBrowse link
G MMP9 matrix metallopeptidase 9 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr20:46,008,908...46,016,561
Ensembl chr20:46,008,908...46,016,561
JBrowse link
G MPO myeloperoxidase EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr17:58,269,855...58,280,935
Ensembl chr17:58,269,855...58,280,935
JBrowse link
G MYD88 MYD88 innate immune signal transduction adaptor EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 3:38,138,661...38,143,022
Ensembl chr 3:38,138,478...38,143,022
JBrowse link
G NFE2L2 nuclear factor, erythroid 2 like 2 treatment EXP
ISO
CTD Direct Evidence: marker/mechanism CTD PMID:30026087, PMID:31900718 RGD:21201303 NCBI chr 2:177,230,303...177,265,131
Ensembl chr 2:177,227,595...177,392,697
JBrowse link
G NOS2 nitric oxide synthase 2 EXP CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr17:27,756,766...27,800,529
Ensembl chr17:27,756,766...27,800,529
JBrowse link
G NOS3 nitric oxide synthase 3 EXP CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 7:150,991,017...151,014,588
Ensembl chr 7:150,991,017...151,014,588
JBrowse link
G NR1H4 nuclear receptor subfamily 1 group H member 4 treatment
disease_progression
ISO
IMP
mRNA:increased expression:liver (rat)
protein:increased expression:liver (rat)
human gene in mouse model
RGD PMID:14623915, PMID:29360226, PMID:29138817, PMID:22057115 RGD:1625205, RGD:14995480, RGD:15042871, RGD:14928333 NCBI chr12:100,473,866...100,564,414
Ensembl chr12:100,473,708...100,564,414
JBrowse link
G PDGFRB platelet derived growth factor receptor beta treatment ISO RGD PMID:18466260 RGD:10449503 NCBI chr 5:150,113,839...150,155,845
Ensembl chr 5:150,113,839...150,155,872
JBrowse link
G PTN pleiotrophin ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr 7:137,227,341...137,343,733
Ensembl chr 7:137,227,341...137,343,774
JBrowse link
G RELA RELA proto-oncogene, NF-kB subunit EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr11:65,653,601...65,662,946
Ensembl chr11:65,653,597...65,663,090
JBrowse link
G SETD7 SET domain containing 7, histone lysine methyltransferase treatment ISO RGD PMID:24097032 RGD:9491846 NCBI chr 4:139,492,974...139,556,219
Ensembl chr 4:139,495,941...139,606,699
JBrowse link
G SLC22A1 solute carrier family 22 member 1 ISO protein:decreased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr 6:160,121,808...160,160,590
Ensembl chr 6:160,121,815...160,158,718
JBrowse link
G SLC22A2 solute carrier family 22 member 2 ISO protein:increased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr 6:160,216,755...160,258,821
Ensembl chr 6:160,171,061...160,277,638
JBrowse link
G TGFB1 transforming growth factor beta 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr19:41,330,323...41,353,922
Ensembl chr19:41,301,587...41,353,922
JBrowse link
G TIMP1 TIMP metallopeptidase inhibitor 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr  X:47,582,408...47,586,789
Ensembl chr  X:47,582,408...47,586,789
JBrowse link
G TIMP2 TIMP metallopeptidase inhibitor 2 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr17:78,852,977...78,925,387
Ensembl chr17:78,852,977...78,925,387
JBrowse link
G TLR4 toll like receptor 4 EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 9:117,704,403...117,724,735
Ensembl chr 9:117,704,175...117,724,735
JBrowse link
G TNF tumor necrosis factor EXP CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 6:31,575,565...31,578,336
Ensembl chr 6:31,575,565...31,578,336
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18836
    disease of anatomical entity 17322
      gastrointestinal system disease 4593
        biliary tract disease 447
          bile duct disease 415
            cholestasis 318
              extrahepatic cholestasis 50
Path 2
Term Annotations click to browse term
  disease 18836
    disease of anatomical entity 17322
      gastrointestinal system disease 4593
        hepatobiliary disease 2551
          biliary tract disease 447
            bile duct disease 415
              cholestasis 318
                extrahepatic cholestasis 50
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.