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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_004936559:7,177,887...7,312,660 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_004936472:14,396,986...14,624,597 JBrowse link
G Acta2 actin alpha 2, smooth muscle ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936735:266,918...283,858 JBrowse link
G Ccn2 cellular communication network factor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936560:42,561...45,748 JBrowse link
G Cd68 CD68 molecule ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936595:858,289...861,131 JBrowse link
G Col1a1 collagen type I alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936490:11,448,552...11,465,836 JBrowse link
G Col3a1 collagen type III alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936506:8,886,494...8,923,921 JBrowse link
G Crh corticotropin releasing hormone ISO protein:decreased expression:hypothalamus (rat) RGD PMID:8387536 RGD:5490980 NCBI chrNW_004936496:7,759,656...7,761,555 JBrowse link
G Cygb cytoglobin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004936594:1,602,436...1,613,783 JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936488:4,384,710...4,388,118 JBrowse link
G Gjb1 gap junction protein beta 1 ISO mRNA,protein:decreased expression:liver: RGD PMID:7762611 RGD:7349397 NCBI chrNW_004936762:389,655...398,035 JBrowse link
G Gjb2 gap junction protein beta 2 ISO RGD PMID:7762611 RGD:7349397 NCBI chrNW_004936720:1,528,205...1,530,296 JBrowse link
G Hamp hepcidin antimicrobial peptide ISO mRNA:decreased expression:liver RGD PMID:19652645 RGD:11041639 NCBI chrNW_004936570:1,009,344...1,010,654 JBrowse link
G Hmgb1 high mobility group box 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936472:25,236,728...25,246,585 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_004936627:4,451,847...4,473,163 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_004936668:62,103...81,549 JBrowse link
G Il1b interleukin 1 beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936783:1,251,678...1,256,807 JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936522:3,034,364...3,037,632 JBrowse link
G Keap1 kelch like ECH associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004936659:785,059...793,775 JBrowse link
G Lgals1 galectin 1 ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chrNW_004936492:3,407,704...3,411,197 JBrowse link
G LOC101963150 sterol 26-hydroxylase, mitochondrial treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chrNW_004936569:1,213,700...1,250,181 JBrowse link
G LOC101970910 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_004936496:4,599,138...4,605,653 JBrowse link
G LOC101977223 7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxylase treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chrNW_004936695:2,263,868...2,265,373 JBrowse link
G Map3k7 mitogen-activated protein kinase kinase kinase 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936510:1,772,971...1,836,075 JBrowse link
G Mapk1 mitogen-activated protein kinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936619:1,889,841...1,932,646 JBrowse link
G Mapk14 mitogen-activated protein kinase 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004936476:23,237,762...23,310,211 JBrowse link
G Mapk3 mitogen-activated protein kinase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936501:12,342,670...12,390,650 JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936728:1,775,746...1,893,895 JBrowse link
G Mapk9 mitogen-activated protein kinase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936739:551,678...602,027 JBrowse link
G Mmp2 matrix metallopeptidase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936475:7,801,356...7,825,831 JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936514:7,038,240...7,045,873 JBrowse link
G Mpo myeloperoxidase ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936490:4,809,773...4,819,070 JBrowse link
G Myd88 MYD88 innate immune signal transduction adaptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936473:27,672,237...27,676,339 JBrowse link
G Nfe2l2 nuclear factor, erythroid 2 like 2 treatment ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:30026087, PMID:31900718 RGD:21201303 NCBI chrNW_004936509:6,589,967...6,621,171 JBrowse link
G Nos2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004936538:4,052,277...4,097,051 JBrowse link
G Nos3 nitric oxide synthase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chrNW_004936527:6,427,147...6,445,770 JBrowse link
G Nr1h4 nuclear receptor subfamily 1 group H member 4 disease_progression
treatment
ISO human gene in mouse model
protein:increased expression:liver (rat)
mRNA:increased expression:liver (rat)
RGD PMID:14623915, PMID:22057115, PMID:29138817, PMID:29360226 RGD:14928333, RGD:14995480, RGD:15042871, RGD:1625205 NCBI chrNW_004936492:13,315,265...13,365,186 JBrowse link
G Pdgfrb platelet derived growth factor receptor beta treatment ISO RGD PMID:18466260 RGD:10449503 NCBI chrNW_004936504:4,762,251...4,799,789 JBrowse link
G Ptn pleiotrophin ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chrNW_004936592:1,706,979...1,806,345 JBrowse link
G Rela RELA proto-oncogene, NF-kB subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chrNW_004936599:3,800,142...3,810,583 JBrowse link
G Setd7 SET domain containing 7, histone lysine methyltransferase treatment ISO RGD PMID:24097032 RGD:9491846 NCBI chrNW_004936535:8,094,479...8,143,108 JBrowse link
G Slc22a1 solute carrier family 22 member 1 ISO protein:decreased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chrNW_004936489:11,534,095...11,556,759 JBrowse link
G Slc22a2 solute carrier family 22 member 2 ISO protein:increased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chrNW_004936489:11,605,403...11,627,786 JBrowse link
G Tgfb1 transforming growth factor beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chrNW_004936661:3,742,080...3,758,266 JBrowse link
G Timp1 TIMP metallopeptidase inhibitor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936502:13,345,936...13,350,170 JBrowse link
G Timp2 TIMP metallopeptidase inhibitor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936594:3,232,433...3,244,241 JBrowse link
G Tlr4 toll like receptor 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936487:6,519,140...6,532,018 JBrowse link
G Tnf tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chrNW_004936727:1,936,066...1,937,766 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 11943
    disease of anatomical entity 11504
      gastrointestinal system disease 3775
        biliary tract disease 379
          bile duct disease 350
            cholestasis 266
              extrahepatic cholestasis 48
Path 2
Term Annotations click to browse term
  disease 11943
    disease of anatomical entity 11504
      gastrointestinal system disease 3775
        hepatobiliary disease 2114
          biliary tract disease 379
            bile duct disease 350
              cholestasis 266
                extrahepatic cholestasis 48
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.