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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, sub-family A (ABC1), member 1 ISO mRNA,protein:increased expression:liver, basolateral plasma membrane (rat) RGD PMID:28660384 RGD:21203516 NCBI chr 4:53,030,789...53,159,988
Ensembl chr 4:53,030,787...53,159,895
JBrowse link
G Abcc4 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 treatment ISO mRNA:increased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr14:118,482,692...118,707,856
Ensembl chr14:118,482,692...118,706,219
JBrowse link
G Acta2 actin, alpha 2, smooth muscle, aorta ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr19:34,240,336...34,255,585
Ensembl chr19:34,241,090...34,255,590
JBrowse link
G Alb albumin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 5:90,460,870...90,476,602
Ensembl chr 5:90,460,897...90,476,602
JBrowse link
G Ccn2 cellular communication network factor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr10:24,595,442...24,598,683
Ensembl chr10:24,595,442...24,598,683
JBrowse link
G Cd68 CD68 antigen ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:69,664,213...69,666,170
Ensembl chr11:69,664,213...69,666,153
JBrowse link
G Col1a1 collagen, type I, alpha 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:94,936,224...94,953,042
Ensembl chr11:94,936,224...94,953,042
JBrowse link
G Col3a1 collagen, type III, alpha 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 1:45,311,538...45,349,706
Ensembl chr 1:45,311,538...45,349,706
JBrowse link
G Crh corticotropin releasing hormone ISO protein:decreased expression:hypothalamus (rat) RGD PMID:8387536 RGD:5490980 NCBI chr 3:19,693,401...19,695,396
Ensembl chr 3:19,693,401...19,695,396
JBrowse link
G Cygb cytoglobin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr11:116,645,595...116,654,504
Ensembl chr11:116,645,595...116,654,313
JBrowse link
G Cyp27a1 cytochrome P450, family 27, subfamily a, polypeptide 1 treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr 1:74,713,148...74,737,897
Ensembl chr 1:74,713,574...74,737,892
JBrowse link
G Cyp7a1 cytochrome P450, family 7, subfamily a, polypeptide 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 4:6,265,612...6,275,632
Ensembl chr 4:6,265,612...6,275,633
JBrowse link
G Cyp8b1 cytochrome P450, family 8, subfamily b, polypeptide 1 treatment ISO mRNA:decreased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr 9:121,914,356...121,916,305
Ensembl chr 9:121,914,356...121,916,305
JBrowse link
G Fos FBJ osteosarcoma oncogene ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr12:85,473,890...85,477,274
Ensembl chr12:85,473,890...85,477,273
JBrowse link
G Gjb1 gap junction protein, beta 1 ISO mRNA,protein:decreased expression:liver: RGD PMID:7762611 RGD:7349397 NCBI chr  X:101,376,376...101,385,629
Ensembl chr  X:101,376,378...101,385,629
JBrowse link
G Gjb2 gap junction protein, beta 2 ISO RGD PMID:7762611 RGD:7349397 NCBI chr14:57,098,602...57,104,702
Ensembl chr14:57,098,600...57,104,702
JBrowse link
G Hamp hepcidin antimicrobial peptide ISO mRNA:decreased expression:liver RGD PMID:19652645 RGD:11041639 NCBI chr 7:30,942,368...30,944,029
Ensembl chr 7:30,942,368...30,944,032
JBrowse link
G Hmgb1 high mobility group box 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:149,046,702...149,053,057
Ensembl chr 5:149,046,702...149,184,489
JBrowse link
G Hmgcs2 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 ISO mRNA, protein:decreased expression:liver, mitochondrion (rat) RGD PMID:12399220 RGD:2326121 NCBI chr 3:98,280,431...98,310,738
Ensembl chr 3:98,280,435...98,310,738
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 chr 5:114,948,980...114,971,062
Ensembl chr 5:114,948,980...114,971,094
JBrowse link
G Il1b interleukin 1 beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 2:129,364,569...129,371,164
Ensembl chr 2:129,364,570...129,371,139
JBrowse link
G Il6 interleukin 6 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:30,013,114...30,019,975
Ensembl chr 5:30,013,114...30,019,981
JBrowse link
G Jun jun proto-oncogene ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 4:95,049,036...95,052,222
Ensembl chr 4:95,049,034...95,052,222
JBrowse link
G Keap1 kelch-like ECH-associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 9:21,229,730...21,239,332
Ensembl chr 9:21,229,730...21,239,361
JBrowse link
G Lgals1 lectin, galactose binding, soluble 1 ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr15:78,926,725...78,930,465
Ensembl chr15:78,926,725...78,930,465
JBrowse link
G Map3k7 mitogen-activated protein kinase kinase kinase 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 4:31,963,492...32,023,470
Ensembl chr 4:31,964,097...32,023,467
JBrowse link
G Mapk1 mitogen-activated protein kinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr16:16,983,382...17,047,453
Ensembl chr16:16,983,382...17,047,453
JBrowse link
G Mapk14 mitogen-activated protein kinase 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr17:28,691,342...28,748,405
Ensembl chr17:28,691,329...28,748,406
JBrowse link
G Mapk3 mitogen-activated protein kinase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 7:126,759,626...126,765,816
Ensembl chr 7:126,759,601...126,765,819
JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr14:33,377,898...33,447,353
Ensembl chr14:33,377,898...33,447,158
JBrowse link
G Mapk9 mitogen-activated protein kinase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:49,846,728...49,886,421
Ensembl chr11:49,846,751...49,886,421
JBrowse link
G Mmp2 matrix metallopeptidase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 8:92,827,290...92,853,421
Ensembl chr 8:92,827,291...92,853,420
JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 2:164,940,326...164,955,850
Ensembl chr 2:164,940,780...164,955,850
JBrowse link
G Mpo myeloperoxidase ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:87,793,784...87,804,412
Ensembl chr11:87,793,581...87,804,413
JBrowse link
G Myd88 myeloid differentiation primary response gene 88 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 9:119,335,934...119,340,018
Ensembl chr 9:119,335,934...119,341,411
JBrowse link
G Nfe2l2 nuclear factor, erythroid derived 2, like 2 treatment ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087, PMID:31900718 RGD:21201303 NCBI chr 2:75,675,513...75,704,663
Ensembl chr 2:75,675,513...75,704,641
JBrowse link
G Nos2 nitric oxide synthase 2, inducible ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr11:78,920,787...78,960,226
Ensembl chr11:78,920,787...78,960,254
JBrowse link
G Nos3 nitric oxide synthase 3, endothelial cell ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 5:24,364,816...24,384,474
Ensembl chr 5:24,364,810...24,384,474
JBrowse link
G Nr1h4 nuclear receptor subfamily 1, group H, member 4 treatment
disease_progression
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 chr10:89,454,234...89,533,645
Ensembl chr10:89,454,234...89,533,585
JBrowse link
G Pdgfrb platelet derived growth factor receptor, beta polypeptide treatment ISO RGD PMID:18466260 RGD:10449503 NCBI chr18:61,045,127...61,085,067
Ensembl chr18:61,045,150...61,085,061
JBrowse link
G Ptn pleiotrophin ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr 6:36,714,924...36,810,179
Ensembl chr 6:36,714,929...36,810,220
JBrowse link
G Rela v-rel reticuloendotheliosis viral oncogene homolog A (avian) ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr19:5,637,442...5,648,134
Ensembl chr19:5,637,483...5,648,130
JBrowse link
G Setd7 SET domain containing (lysine methyltransferase) 7 treatment ISO RGD PMID:24097032 RGD:9491846 NCBI chr 3:51,515,318...51,560,823
Ensembl chr 3:51,515,319...51,560,879
JBrowse link
G Slc22a1 solute carrier family 22 (organic cation transporter), member 1 ISO protein:decreased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr17:12,648,874...12,675,838
Ensembl chr17:12,648,869...12,675,829
JBrowse link
G Slc22a2 solute carrier family 22 (organic cation transporter), member 2 ISO protein:increased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr17:12,584,189...12,628,489
Ensembl chr17:12,584,132...12,628,488
JBrowse link
G Tgfb1 transforming growth factor, beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr 7:25,687,002...25,705,077
Ensembl chr 7:25,687,002...25,705,077
JBrowse link
G Timp1 tissue inhibitor of metalloproteinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr  X:20,870,166...20,874,737
Ensembl chr  X:20,870,166...20,874,735
JBrowse link
G Timp2 tissue inhibitor of metalloproteinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:118,301,061...118,355,411
Ensembl chr11:118,301,069...118,355,740
JBrowse link
G Tlr4 toll-like receptor 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 4:66,827,551...66,846,581
Ensembl chr 4:66,827,584...66,930,284
JBrowse link
G Tnf tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr17:35,199,367...35,202,007
Ensembl chr17:35,199,381...35,202,007
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 13400
    disease of anatomical entity 12876
      gastrointestinal system disease 4317
        biliary tract disease 444
          bile duct disease 413
            cholestasis 317
              extrahepatic cholestasis 50
Path 2
Term Annotations click to browse term
  disease 13400
    disease of anatomical entity 12876
      gastrointestinal system disease 4317
        hepatobiliary disease 2490
          biliary tract disease 444
            bile duct disease 413
              cholestasis 317
                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.