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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 chrNW_004955419:21,553,863...21,681,626
Ensembl chrNW_004955419:21,553,835...21,681,619
JBrowse link
G Abcc4 ATP binding cassette subfamily C member 4 treatment ISO mRNA:increased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chrNW_004955404:14,700,808...14,927,944
Ensembl chrNW_004955404:14,700,808...14,928,617
JBrowse link
G Acta2 actin alpha 2, smooth muscle ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955425:4,023,001...4,039,980
Ensembl chrNW_004955425:4,026,430...4,040,747
JBrowse link
G Alb albumin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004955447:9,327...21,212 JBrowse link
G Ccn2 cellular communication network factor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955436:12,523,602...12,526,986
Ensembl chrNW_004955436:12,522,944...12,526,480
JBrowse link
G Cd68 CD68 molecule ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955467:9,340,490...9,343,912
Ensembl chrNW_004955467:9,341,364...9,343,836
JBrowse link
G Col1a1 collagen type I alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955451:11,468,156...11,484,410
Ensembl chrNW_004955451:11,468,290...11,483,073
JBrowse link
G Col3a1 collagen type III alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955403:9,720,831...9,758,019
Ensembl chrNW_004955403:9,721,114...9,757,887
JBrowse link
G Crh corticotropin releasing hormone ISO protein:decreased expression:hypothalamus (rat) RGD PMID:8387536 RGD:5490980 NCBI chrNW_004955444:12,989,210...12,991,300 JBrowse link
G Cygb cytoglobin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004955506:5,766,006...5,775,722
Ensembl chrNW_004955506:5,766,006...5,775,784
JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955523:307,181...310,728
Ensembl chrNW_004955523:305,728...310,728
JBrowse link
G Gjb1 gap junction protein beta 1 ISO mRNA,protein:decreased expression:liver: RGD PMID:7762611 RGD:7349397 NCBI chrNW_004955475:10,779,415...10,787,910
Ensembl chrNW_004955475:10,785,996...10,787,910
JBrowse link
G Gjb2 gap junction protein beta 2 ISO RGD PMID:7762611 RGD:7349397 NCBI chrNW_004955497:987,213...989,477
Ensembl chrNW_004955497:988,422...989,099
JBrowse link
G Hamp hepcidin antimicrobial peptide ISO mRNA:decreased expression:liver RGD PMID:19652645 RGD:11041639 NCBI chrNW_004955468:4,576,080...4,577,591
Ensembl chrNW_004955468:4,575,510...4,577,649
JBrowse link
G Hmgb1 high mobility group box 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955431:15,373,207...15,377,339 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 chrNW_004955435:22,804,484...22,820,807
Ensembl chrNW_004955435:22,804,484...22,821,482
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 chrNW_004955455:10,694,102...10,717,613
Ensembl chrNW_004955455:10,694,102...10,717,613
JBrowse link
G Il1b interleukin 1 beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955470:1,486,936...1,491,888
Ensembl chrNW_004955470:1,486,967...1,491,947
JBrowse link
G Il6 interleukin 6 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955410:25,079,835...25,084,390 JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955464:1,107,598...1,110,326 JBrowse link
G Keap1 kelch like ECH associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004955495:1,704,695...1,711,339
Ensembl chrNW_004955495:1,704,695...1,711,290
JBrowse link
G Lgals1 galectin 1 ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chrNW_004955413:24,072,086...24,075,452
Ensembl chrNW_004955413:24,072,086...24,075,452
JBrowse link
G LOC102004889 sterol 26-hydroxylase, mitochondrial treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chrNW_004955453:14,601,495...14,647,383
Ensembl chrNW_004955453:14,601,444...14,647,366
JBrowse link
G LOC102008593 cholesterol 7-alpha-monooxygenase treatment ISO mRNA:decreased expression:liver, nucleus (rat)
mRNA:decreased expression:liver (rat)
RGD PMID:28660384, PMID:29360226 RGD:14995480, RGD:21203516 NCBI chrNW_004955454:17,035,105...17,078,854
Ensembl chrNW_004955454:17,036,204...17,042,756
JBrowse link
G LOC102019604 7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxylase treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chrNW_004955420:27,988,067...27,990,637 JBrowse link
G Map3k7 mitogen-activated protein kinase kinase kinase 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955411:17,177,335...17,229,957
Ensembl chrNW_004955411:17,177,335...17,229,957
JBrowse link
G Mapk1 mitogen-activated protein kinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955442:17,284,232...17,380,026
Ensembl chrNW_004955442:17,284,232...17,380,020
JBrowse link
G Mapk14 mitogen-activated protein kinase 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004955437:3,836,331...3,884,083
Ensembl chrNW_004955437:3,838,232...3,884,083
JBrowse link
G Mapk3 mitogen-activated protein kinase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955493:6,870,699...6,876,836
Ensembl chrNW_004955493:6,869,668...6,879,152
JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955556:1,593,552...1,705,543
Ensembl chrNW_004955556:1,593,494...1,665,784
JBrowse link
G Mapk9 mitogen-activated protein kinase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955408:391,094...430,638
Ensembl chrNW_004955408:391,094...430,981
JBrowse link
G Mmp2 matrix metallopeptidase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955433:13,024,844...13,050,041
Ensembl chrNW_004955433:13,024,418...13,052,775
JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955445:11,295,500...11,303,322
Ensembl chrNW_004955445:11,295,448...11,303,288
JBrowse link
G Mpo myeloperoxidase ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955451:4,743,744...4,753,358
Ensembl chrNW_004955451:4,743,744...4,753,358
JBrowse link
G Myd88 MYD88 innate immune signal transduction adaptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955427:25,553,589...25,557,654
Ensembl chrNW_004955427:25,553,589...25,559,138
JBrowse link
G Nfe2l2 nuclear factor, erythroid 2 like 2 treatment ISO CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:30026087, PMID:31900718 RGD:21201303 NCBI chrNW_004955403:19,510,122...19,536,428
Ensembl chrNW_004955403:19,532,103...19,535,944
JBrowse link
G Nos2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004955481:5,197,957...5,232,406
Ensembl chrNW_004955481:5,201,234...5,231,961
JBrowse link
G Nos3 nitric oxide synthase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004955491:5,438,228...5,457,308
Ensembl chrNW_004955491:5,438,010...5,460,814
JBrowse link
G Nr1h4 nuclear receptor subfamily 1 group H member 4 disease_progression
treatment
ISO protein:increased expression:liver (rat)
mRNA:increased expression:liver (rat)
human gene in mouse model
RGD PMID:14623915, PMID:22057115, PMID:29138817, PMID:29360226 RGD:14928333, RGD:14995480, RGD:15042871, RGD:1625205 NCBI chrNW_004955405:36,160,360...36,236,258
Ensembl chrNW_004955405:36,160,049...36,237,751
JBrowse link
G Pdgfrb platelet derived growth factor receptor beta treatment ISO RGD PMID:18466260 RGD:10449503 NCBI chrNW_004955415:4,365,848...4,403,317
Ensembl chrNW_004955415:4,365,743...4,403,587
JBrowse link
G Ptn pleiotrophin ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chrNW_004955494:5,580,264...5,681,848
Ensembl chrNW_004955494:5,580,422...5,684,190
JBrowse link
G Rela RELA proto-oncogene, NF-kB subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chrNW_004955422:19,602,930...19,612,263
Ensembl chrNW_004955422:19,603,345...19,611,516
JBrowse link
G Setd7 SET domain containing 7, histone lysine methyltransferase treatment ISO RGD PMID:24097032 RGD:9491846 NCBI chrNW_004955428:4,131,431...4,178,250
Ensembl chrNW_004955428:4,131,103...4,178,250
JBrowse link
G Slc22a2 solute carrier family 22 member 2 ISO protein:increased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chrNW_004955439:20,567,241...20,608,281
Ensembl chrNW_004955439:20,567,212...20,609,105
JBrowse link
G Tgfb1 transforming growth factor beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chrNW_004955555:274,405...288,441
Ensembl chrNW_004955555:270,652...288,441
JBrowse link
G Timp1 TIMP metallopeptidase inhibitor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955516:507,113...511,360
Ensembl chrNW_004955516:505,789...512,118
JBrowse link
G Timp2 TIMP metallopeptidase inhibitor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955506:3,769,113...3,812,896
Ensembl chrNW_004955506:3,768,646...3,813,820
JBrowse link
G Tlr4 toll like receptor 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955419:10,190,937...10,201,896
Ensembl chrNW_004955419:10,191,120...10,202,135
JBrowse link
G Tnf tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004955437:117,267...119,899
Ensembl chrNW_004955437:117,206...120,700
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 11815
    disease of anatomical entity 11368
      gastrointestinal system disease 3751
        biliary tract disease 375
          bile duct disease 348
            cholestasis 266
              extrahepatic cholestasis 49
Path 2
Term Annotations click to browse term
  disease 11815
    disease of anatomical entity 11368
      gastrointestinal system disease 3751
        hepatobiliary disease 2099
          biliary tract disease 375
            bile duct disease 348
              cholestasis 266
                extrahepatic cholestasis 49
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.