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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 chr11:60,761,669...60,869,753
Ensembl chr11:60,761,655...60,890,496
JBrowse link
G ABCC4 ATP binding cassette subfamily C member 4 treatment ISO mRNA:increased expression:liver (rat) RGD PMID:29360226 RGD:14995480 NCBI chr22:45,767,033...46,013,577
Ensembl chr22:45,765,835...46,013,505
JBrowse link
G ACTA2 actin alpha 2, smooth muscle ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr26:38,700,434...38,714,915
Ensembl chr26:38,700,480...38,711,753
JBrowse link
G ALB albumin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr13:62,133,747...62,169,349
Ensembl chr13:62,053,814...62,294,709
JBrowse link
G B9D2 B9 domain containing 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr 1:112,621,832...112,627,726
Ensembl chr 1:112,621,633...112,643,885
JBrowse link
G CCN2 cellular communication network factor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 1:25,508,082...25,511,058
Ensembl chr 1:25,507,662...25,510,145
JBrowse link
G CD68 CD68 molecule ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:32,500,899...32,503,355
Ensembl chr 5:32,501,380...32,503,183
JBrowse link
G COL1A1 collagen type I alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 9:26,183,852...26,199,927
Ensembl chr 9:26,183,852...26,199,927
JBrowse link
G COL3A1 collagen type III alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr36:30,488,250...30,526,367
Ensembl chr36:30,488,488...30,536,765
JBrowse link
G CRH corticotropin releasing hormone ISO protein:decreased expression:hypothalamus (rat) RGD PMID:8387536 RGD:5490980 NCBI chr29:15,831,944...15,840,560
Ensembl chr29:15,831,944...15,834,384
JBrowse link
G CYGB cytoglobin ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 9:4,191,114...4,201,438
Ensembl chr 9:4,184,959...4,200,164
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 chr37:25,366,475...25,401,978
Ensembl chr37:25,366,472...25,401,509
JBrowse link
G CYP7A1 cytochrome P450 family 7 subfamily A member 1 treatment ISO mRNA:decreased expression:liver, nucleus (rat)
mRNA:decreased expression:liver (rat)
RGD PMID:28660384, PMID:29360226 RGD:14995480, RGD:21203516 NCBI chr29:9,285,315...9,295,895
Ensembl chr29:9,286,181...9,332,310
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 chr23:11,965,685...11,968,994
Ensembl chr23:11,967,341...11,968,846
JBrowse link
G FOS Fos proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 8:48,330,856...48,334,273
Ensembl chr 8:48,331,026...48,333,467
JBrowse link
G GJB1 gap junction protein beta 1 ISO mRNA,protein:decreased expression:liver: RGD PMID:7762611 RGD:7349397 NCBI chr  X:55,565,995...55,575,332
Ensembl chr  X:55,573,808...55,574,659
JBrowse link
G GJB2 gap junction protein beta 2 ISO RGD PMID:7762611 RGD:7349397 NCBI chr25:17,952,851...17,958,289
Ensembl chr25:17,952,851...17,958,289
JBrowse link
G HAMP hepcidin antimicrobial peptide ISO mRNA:decreased expression:liver RGD PMID:19652645 RGD:11041639 NCBI chr 1:117,305,531...117,306,587
Ensembl chr 1:117,305,411...117,306,619
JBrowse link
G HMGB1 high mobility group box 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr25:9,431,223...9,558,167
Ensembl chr25:9,431,218...9,558,165
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 chr17:56,679,942...56,698,521
Ensembl chr17:56,680,301...56,698,419
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 chr26:16,805,690...16,826,065
Ensembl chr26:16,805,690...16,824,790
JBrowse link
G IL1B interleukin 1 beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr17:37,019,329...37,033,388
Ensembl chr17:37,019,329...37,024,458
JBrowse link
G IL6 interleukin 6 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr14:36,474,268...36,478,519
Ensembl chr14:36,473,394...36,478,519
JBrowse link
G JUN Jun proto-oncogene, AP-1 transcription factor subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 5:50,966,698...50,968,939 JBrowse link
G KEAP1 kelch like ECH associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr20:50,651,070...50,661,178
Ensembl chr20:50,650,711...50,658,496
JBrowse link
G LGALS1 galectin 1 ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr10:26,932,351...26,935,580
Ensembl chr10:26,932,301...26,935,646
JBrowse link
G MAP3K7 mitogen-activated protein kinase kinase kinase 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr12:49,669,849...49,740,039
Ensembl chr12:49,672,389...49,739,850
JBrowse link
G MAPK1 mitogen-activated protein kinase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr26:31,013,607...31,132,998
Ensembl chr26:31,013,607...31,132,998
JBrowse link
G MAPK14 mitogen-activated protein kinase 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr12:5,145,647...5,221,558
Ensembl chr12:5,146,037...5,220,603
JBrowse link
G MAPK3 mitogen-activated protein kinase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 6:18,109,184...18,115,728
Ensembl chr 6:18,109,222...18,114,425
JBrowse link
G MAPK8 mitogen-activated protein kinase 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr28:323,361...410,367
Ensembl chr28:368,513...406,401
JBrowse link
G MAPK9 mitogen-activated protein kinase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:1,443,528...1,480,501
Ensembl chr11:1,443,547...1,478,119
JBrowse link
G MMP2 matrix metallopeptidase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 2:60,471,092...60,492,991
Ensembl chr 2:60,471,257...60,494,113
JBrowse link
G MMP9 matrix metallopeptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr24:33,274,260...33,281,116
Ensembl chr24:33,274,268...33,281,293
JBrowse link
G MPO myeloperoxidase ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 9:32,927,483...32,938,007
Ensembl chr 9:32,927,483...32,937,820
JBrowse link
G MYD88 MYD88 innate immune signal transduction adaptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr23:7,901,578...7,905,274
Ensembl chr23:7,901,250...7,904,534
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 chr36:20,989,205...21,087,044
Ensembl chr36:20,989,360...21,012,524
JBrowse link
G NOS2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr 9:42,171,821...42,210,217
Ensembl chr 9:42,171,821...42,208,588
JBrowse link
G NOS3 nitric oxide synthase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30026087 NCBI chr16:15,054,196...15,072,454
Ensembl chr16:15,011,344...15,072,277
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 chr15:39,497,313...39,608,120
Ensembl chr15:39,536,290...39,608,116
JBrowse link
G PDGFRB platelet derived growth factor receptor beta treatment ISO RGD PMID:18466260 RGD:10449503 NCBI chr 4:58,925,922...58,963,639
Ensembl chr 4:58,926,351...58,962,283
JBrowse link
G PTN pleiotrophin ISO mRNA:increased expression:liver (rat) RGD PMID:18225978 RGD:2316551 NCBI chr16:11,283,078...11,382,820
Ensembl chr16:11,283,077...11,382,814
JBrowse link
G RELA RELA proto-oncogene, NF-kB subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951, PMID:30026087 NCBI chr18:51,550,003...51,558,861
Ensembl chr18:51,550,040...51,558,875
JBrowse link
G SETD7 SET domain containing 7, histone lysine methyltransferase treatment ISO RGD PMID:24097032 RGD:9491846 NCBI chr19:3,186,620...3,229,305
Ensembl chr19:3,186,906...3,224,113
JBrowse link
G SLC22A1 solute carrier family 22 member 1 ISO protein:decreased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr 1:49,268,978...49,296,522 JBrowse link
G SLC22A2 solute carrier family 22 member 2 ISO protein:increased expression:kidney RGD PMID:20814153 RGD:7243879 NCBI chr 1:49,327,621...49,348,435
Ensembl chr 1:49,327,296...49,348,435
JBrowse link
G TIMP1 TIMP metallopeptidase inhibitor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr  X:41,201,623...41,205,314
Ensembl chr  X:41,201,638...41,205,310
JBrowse link
G TIMP2 TIMP metallopeptidase inhibitor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr 9:2,521,882...2,533,883
Ensembl chr 9:2,521,882...2,533,989
JBrowse link
G TLR4 toll like receptor 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr11:71,356,390...71,367,166
Ensembl chr11:71,356,390...71,367,165
JBrowse link
G TNF tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:28789951 NCBI chr12:1,074,561...1,076,425
Ensembl chr12:1,074,552...1,076,425
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 12680
    disease of anatomical entity 12218
      gastrointestinal system disease 4063
        biliary tract disease 411
          bile duct disease 382
            cholestasis 297
              extrahepatic cholestasis 50
Path 2
Term Annotations click to browse term
  disease 12680
    disease of anatomical entity 12218
      gastrointestinal system disease 4063
        hepatobiliary disease 2318
          biliary tract disease 411
            bile duct disease 382
              cholestasis 297
                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.