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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 IEP mRNA,protein:increased expression:liver, basolateral plasma membrane (rat) RGD PMID:28660384 RGD:21203516 NCBI chr 5:69,857,717...69,983,042
Ensembl chr 5:69,857,771...69,983,015
JBrowse link
G Abcc4 ATP binding cassette subfamily C member 4 treatment IEP mRNA:increased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr15:103,695,415...103,927,980
Ensembl chr15:103,696,557...103,927,592
JBrowse link
G Acta2 actin alpha 2, smooth muscle ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 1:252,537,614...252,550,394
Ensembl chr 1:252,537,615...252,550,394
JBrowse link
G Alb albumin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr14:19,176,275...19,191,793
Ensembl chr14:19,176,277...19,191,863
JBrowse link
G Ccn2 cellular communication network factor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 1:21,851,657...21,854,773
Ensembl chr 1:21,851,660...21,854,773
JBrowse link
G Cd68 Cd68 molecule ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:56,268,726...56,270,605
Ensembl chr10:56,268,720...56,270,640
JBrowse link
G Col1a1 collagen type I alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:82,745,801...82,762,790
Ensembl chr10:82,745,801...82,762,789
JBrowse link
G Col3a1 collagen type III alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 9:52,023,295...52,059,221
Ensembl chr 9:52,023,295...52,059,217
JBrowse link
G Crh corticotropin releasing hormone IEP protein:decreased expression:hypothalamus (rat) RGD PMID:8387536 RGD:5490980 NCBI chr 2:104,459,999...104,461,863
Ensembl chr 2:104,459,999...104,461,863
JBrowse link
G Cygb cytoglobin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr10:105,618,325...105,628,091
Ensembl chr10:105,618,326...105,628,091
JBrowse link
G Cyp27a1 cytochrome P450, family 27, subfamily a, polypeptide 1 treatment IEP mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr 9:81,968,285...81,998,213
Ensembl chr 9:81,968,332...81,998,169
JBrowse link
G Cyp7a1 cytochrome P450 family 7 subfamily A member 1 treatment IEP mRNA:decreased expression:liver (rat)
mRNA:decreased expression:liver, nucleus (rat)
RGD PMID:29360226, PMID:28660384 RGD:14995480, RGD:21203516 NCBI chr 5:19,358,734...19,368,431
Ensembl chr 5:19,358,734...19,368,431
JBrowse link
G Cyp8b1 cytochrome P450 family 8 subfamily B member 1 treatment IEP mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr 8:130,548,418...130,550,388
Ensembl chr 8:130,548,418...130,550,388
JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 6:109,300,433...109,303,299
Ensembl chr 6:109,300,433...109,303,299
JBrowse link
G Gjb1 gap junction protein, beta 1 IEP mRNA,protein:decreased expression:liver: RGD PMID:7762611 RGD:7349397 NCBI chr  X:71,272,030...71,279,973
Ensembl chr  X:71,272,042...71,279,977
JBrowse link
G Gjb2 gap junction protein, beta 2 IEP RGD PMID:7762611 RGD:7349397 NCBI chr15:37,377,313...37,394,494
Ensembl chr15:37,377,316...37,383,277
JBrowse link
G Hamp hepcidin antimicrobial peptide IEP mRNA:decreased expression:liver RGD PMID:19652645 RGD:11041639 NCBI chr 1:89,368,021...89,369,960
Ensembl chr 1:89,368,021...89,369,960
JBrowse link
G Hmgb1 high mobility group box 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr12:7,082,529...7,090,246
Ensembl chr16:37,500,017...37,502,237
JBrowse link
G Hmgcs2 3-hydroxy-3-methylglutaryl-CoA synthase 2 IEP mRNA, protein:decreased expression:liver, mitochondrion (rat) RGD PMID:12399220 RGD:2326121 NCBI chr 2:200,452,623...200,480,785
Ensembl chr 2:200,452,624...200,479,423
JBrowse link
G Hnf1a HNF1 homeobox A IEP mRNA,protein,DNA:decreased expression, decreased binding, decreased expression:liver, nuclear (rat) RGD PMID:15723437 RGD:14700989 NCBI chr12:47,407,811...47,433,342
Ensembl chr12:47,407,811...47,433,342
JBrowse link
G Il1b interleukin 1 beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 3:121,876,256...121,882,637
Ensembl chr 3:121,876,263...121,882,726
JBrowse link
G Il6 interleukin 6 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 4:3,043,231...3,047,807
Ensembl chr 4:3,043,231...3,047,807
JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:114,011,184...114,014,277
Ensembl chr 5:114,011,189...114,014,277
JBrowse link
G Keap1 Kelch-like ECH-associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 8:22,250,518...22,259,868
Ensembl chr 8:22,250,518...22,259,779
JBrowse link
G Lgals1 galectin 1 IEP mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr 7:120,153,184...120,156,290
Ensembl chr 7:120,153,184...120,156,289
JBrowse link
G Map3k7 mitogen activated protein kinase kinase kinase 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:47,183,142...47,244,424
Ensembl chr 5:47,186,558...47,244,416
JBrowse link
G Mapk1 mitogen activated protein kinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:88,203,863...88,273,301
Ensembl chr11:88,211,599...88,273,254
JBrowse link
G Mapk14 mitogen activated protein kinase 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr20:5,933,290...5,995,137
Ensembl chr20:5,933,303...5,995,137
JBrowse link
G Mapk3 mitogen activated protein kinase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 1:198,192,773...198,198,975
Ensembl chr 1:198,192,773...198,198,975
JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr16:9,620,854...9,709,342
Ensembl chr16:9,625,177...9,709,347
JBrowse link
G Mapk9 mitogen-activated protein kinase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:35,333,859...35,374,364
Ensembl chr10:35,333,859...35,374,355
JBrowse link
G Mmp2 matrix metallopeptidase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr19:15,542,771...15,570,589
Ensembl chr19:15,542,765...15,570,611
JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 3:161,413,410...161,421,473
Ensembl chr 3:161,413,298...161,421,520
JBrowse link
G Mpo myeloperoxidase ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:75,087,892...75,098,260
Ensembl chr10:75,087,892...75,098,260
JBrowse link
G Myd88 MYD88, innate immune signal transduction adaptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 8:128,022,512...128,027,462
Ensembl chr 8:128,022,473...128,026,841
JBrowse link
G Nfe2l2 nuclear factor, erythroid 2-like 2 treatment ISO
IEP
CTD Direct Evidence: marker/mechanism CTD PMID:30026087, PMID:31900718 RGD:21201303 NCBI chr 3:62,497,568...62,525,146
Ensembl chr 3:62,497,571...62,524,996
JBrowse link
G Nos2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr10:66,188,290...66,221,621
Ensembl chr10:66,189,786...66,313,190
JBrowse link
G Nos3 nitric oxide synthase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 4:7,321,908...7,342,404
Ensembl chr 4:7,320,668...7,342,410
JBrowse link
G Nr1h4 nuclear receptor subfamily 1, group H, member 4 treatment
disease_progression
IDA
IEP
ISO
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 chr 7:30,003,429...30,162,095
Ensembl chr 7:30,003,429...30,162,056
JBrowse link
G Pdgfrb platelet derived growth factor receptor beta treatment IMP RGD PMID:18466260 RGD:10449503 NCBI chr18:56,364,586...56,406,381
Ensembl chr18:56,364,620...56,406,381
JBrowse link
G Ptn pleiotrophin IEP mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr 4:64,239,156...64,330,996
Ensembl chr 4:64,239,158...64,330,996
JBrowse link
G Rela RELA proto-oncogene, NF-kB subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr 1:220,992,770...221,003,249
Ensembl chr 1:220,992,770...221,003,249
JBrowse link
G Setd7 SET domain containing 7, histone lysine methyltransferase treatment IMP RGD PMID:24097032 RGD:9491846 NCBI chr 2:140,576,188...140,618,405
Ensembl chr 2:140,576,188...140,618,405
JBrowse link
G Slc22a1 solute carrier family 22 member 1 IEP protein:decreased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr 1:48,273,639...48,300,645
Ensembl chr 1:48,273,611...48,300,655
JBrowse link
G Slc22a2 solute carrier family 22 member 2 IEP protein:increased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr 1:48,318,025...48,360,219
Ensembl chr 1:48,317,995...48,360,261
JBrowse link
G Tgfb1 transforming growth factor, beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr 1:82,480,875...82,497,196
Ensembl chr 1:82,480,195...82,497,199
JBrowse link
G Timp1 TIMP metallopeptidase inhibitor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr  X:1,364,771...1,369,451
Ensembl chr  X:1,364,786...1,369,384
JBrowse link
G Timp2 TIMP metallopeptidase inhibitor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:107,338,465...107,386,072
Ensembl chr10:107,338,465...107,386,072
JBrowse link
G Tlr4 toll-like receptor 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:82,587,424...82,601,056
Ensembl chr 5:82,587,420...82,601,052
JBrowse link
G Tnf tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr20:5,189,382...5,192,000
Ensembl chr20:5,189,390...5,192,000
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16045
    disease of anatomical entity 15292
      gastrointestinal system disease 4623
        biliary tract disease 437
          bile duct disease 407
            cholestasis 312
              extrahepatic cholestasis 50
Path 2
Term Annotations click to browse term
  disease 16045
    disease of anatomical entity 15292
      gastrointestinal system disease 4623
        hepatobiliary disease 2496
          biliary tract disease 437
            bile duct disease 407
              cholestasis 312
                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.