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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:bile duct carcinoma
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Accession:DOID:4897 term browser browse the term
Definition:A bile duct cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. (DO)
Synonyms:xref: NCI:C27814
For additional species annotation, visit the Alliance of Genome Resources.


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cholangiocarcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcc2 ATP binding cassette subfamily C member 2 susceptibility ISO DNA:polymorphism:exon:c.3972C>T (human) RGD PMID:19451719 RGD:2317508 NCBI chrNW_004936636:292,631...341,999 JBrowse link
G Adrb2 adrenoceptor beta 2 ISO protein:decreased expression:liver RGD PMID:16292515 RGD:2325640 NCBI chrNW_004936504:5,985,407...5,987,453 JBrowse link
G Alox5 arachidonate 5-lipoxygenase ISO protein:increased expression:bile duct RGD PMID:18507031 RGD:2317521 NCBI chrNW_004936554:7,807,914...7,848,691 JBrowse link
G Anxa2 annexin A2 disease_progression ISO RGD PMID:20493868 RGD:2325728 NCBI chrNW_004936471:21,274,112...21,329,286 JBrowse link
G Apc APC regulator of WNT signaling pathway ISO DNA:loss of heterozygosity
DNA:hypermethylation:promoter
RGD PMID:10212000 PMID:15467712 RGD:2317198 RGD:2317205 NCBI chrNW_004936531:6,899,580...7,019,016 JBrowse link
G Apoa1 apolipoprotein A1 ISO protein:decreased expression:serum RGD PMID:19486127 RGD:2325756 NCBI chrNW_004936542:2,111,055...2,112,626 JBrowse link
G Arid1a AT-rich interaction domain 1A ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936474:11,148,857...11,197,312 JBrowse link
G Asph aspartate beta-hydroxylase ISO RGD PMID:21898484 RGD:6902945 NCBI chrNW_004936496:11,604,992...11,815,680 JBrowse link
G Bap1 BRCA1 associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 PMID:25231345 NCBI chrNW_004936473:3,239,009...3,247,806 JBrowse link
G Braf B-Raf proto-oncogene, serine/threonine kinase ISO DNA:missense mutation:cds:p.V600E (human) RGD PMID:12692057 RGD:11073239 NCBI chrNW_004936592:4,728,371...4,833,830 JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chrNW_004936678:365,005...560,546 JBrowse link
G Epo erythropoietin ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chrNW_004936543:742,722...745,332 JBrowse link
G Epor erythropoietin receptor ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chrNW_004936659:1,468,391...1,473,880 JBrowse link
G Erbb2 erb-b2 receptor tyrosine kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635 NCBI chrNW_004936490:14,887,062...14,910,038 JBrowse link
G Ezh2 enhancer of zeste 2 polycomb repressive complex 2 subunit disease_progression
no_association
ISO DNA:SNP: :g.148505302C>T (rs887569) (human)
DNA:SNPs: :g.148525904C>G, (rs2302427), g.148519011C>T (rs6464926), g.148517456T>G (rs17171119) (human)
RGD PMID:24179546 RGD:126779604 NCBI chrNW_004936527:5,024,077...5,069,152 JBrowse link
G Faslg Fas ligand ISO RGD PMID:11029528 RGD:2317746 NCBI chrNW_004936481:14,789,547...14,795,780 JBrowse link
G Fgfr2 fibroblast growth factor receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936486:10,506,680...10,606,272 JBrowse link
G Fscn1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile ducts RGD PMID:19721413 RGD:2317780 NCBI chrNW_004936765:609,894...619,417 JBrowse link
G Gstp1 glutathione S-transferase pi 1 treatment ISO human cell line in a mouse model
DNA:hypermethylation:promoter
RGD PMID:12805482 PMID:15467712 RGD:14401711 RGD:2317198 NCBI chrNW_004936599:2,197,681...2,200,642 JBrowse link
G Hdac6 histone deacetylase 6 ISO protein:increased expression:liver: RGD PMID:23370327 RGD:9681560 NCBI chrNW_004936721:757,500...778,416 JBrowse link
G Hgf hepatocyte growth factor ISO mRNA, protein:increased expression: :
protein:increased expression:serum
RGD PMID:10827151 PMID:16974053 RGD:2317909 RGD:2317925 NCBI chrNW_004936734:354,798...428,356 JBrowse link
G Idh1 isocitrate dehydrogenase (NADP(+)) 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936950:334,894...349,221 JBrowse link
G Idh2 isocitrate dehydrogenase (NADP(+)) 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936483:15,845,777...15,864,341 JBrowse link
G Il4r interleukin 4 receptor ISO mRNA:increased expression:bile duct RGD PMID:18798553 RGD:2317263 NCBI chrNW_004936501:11,025,590...11,058,807 JBrowse link
G Il6 interleukin 6 ISO protein:increased expression:serum
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:15011822 PMID:17621267 PMID:28925763 RGD:14975292 RGD:2317167 NCBI chrNW_004936549:7,015,595...7,016,246 JBrowse link
G Kmt2c lysine methyltransferase 2C ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936527:7,310,885...7,508,032 JBrowse link
G Kras KRAS proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8968066 PMID:22561520 NCBI chrNW_004936548:2,078,568...2,113,877 JBrowse link
G Krt7 keratin 7 ISO RGD PMID:18393293 RGD:2317308 NCBI chrNW_004936512:9,641,587...9,656,573 JBrowse link
G LOC101963142 mucin-3B ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chrNW_004936543:886,333...904,504 JBrowse link
G LOC101971027 neuroendocrine secretory protein 55 disease_progression ISO DNA:polymorphism:393T>C (human)
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:17356712 PMID:22561520 RGD:1601377 NCBI chrNW_004936530:1,353,432...1,407,437 JBrowse link
G Mdm2 MDM2 proto-oncogene disease_progression ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15619210 RGD:2317417 NCBI chrNW_004936545:6,709,903...6,732,334 JBrowse link
G Met MET proto-oncogene, receptor tyrosine kinase disease_progression ISO protein:increased phosphorylation:liver, carcinoma (human)
protein:increased expression:liver, biliary epithelium (rat)
RGD PMID:14656942 PMID:16818635 RGD:2317578 RGD:2317601 NCBI chrNW_004936589:2,280,803...2,390,179 JBrowse link
G Mgmt O-6-methylguanine-DNA methyltransferase ISO DNA:hypermethylation:promoter (human) RGD PMID:17550320 RGD:2317632 NCBI chrNW_004936486:16,744,607...16,923,209 JBrowse link
G Mki67 marker of proliferation Ki-67 disease_progression ISO RGD PMID:12903495 RGD:2317705 NCBI chrNW_004936486:15,561,327...15,587,109 JBrowse link
G Mmp2 matrix metallopeptidase 2 disease_progression ISO protein:increased expression:bile duct RGD PMID:15213623 PMID:19629755 RGD:2324667 RGD:2325769 NCBI chrNW_004936475:7,801,356...7,825,831 JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO protein:increased expression:bile duct
mRNA:increased expression:bile duct
RGD PMID:15213623 PMID:16463672 RGD:2324667 RGD:2325856 NCBI chrNW_004936514:7,038,240...7,045,873 JBrowse link
G Mthfr methylenetetrahydrofolate reductase susceptibility ISO DNA:polymorphism (human) RGD PMID:17201138 RGD:2317119 NCBI chrNW_004936474:623,438...637,849 JBrowse link
G Muc1 mucin 1, cell surface associated disease_progression ISO protein:increased secretion:bile
protein:increased expression:bile duct:
protein:increased expression:serum
mRNA:increased expression:bile duct
RGD PMID:15213623 PMID:18081149 PMID:19055478 PMID:19260467 PMID:19639217 RGD:2317986 RGD:2324622 RGD:2324638 RGD:2324664 RGD:2324667 NCBI chrNW_004936580:4,691,870...4,694,092 JBrowse link
G Muc16 mucin 16, cell surface associated ISO associated with Opisthorchiasis;protein:increased expression:serum RGD PMID:1653472 RGD:2325142 NCBI chrNW_004936588:5,506,683...5,586,450 JBrowse link
G Muc2 mucin 2, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chrNW_004936816:60,499...91,628 JBrowse link
G Muc4 mucin 4, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:14752841 PMID:19082442 RGD:2303602 RGD:2324944 NCBI chrNW_004936784:515,608...539,915 JBrowse link
G Muc5ac mucin 5AC, oligomeric mucus/gel-forming disease_progression ISO protein:increased expression:serum
mRNA:increased expression:bile duct
RGD PMID:11680592 PMID:14508831 RGD:2324948 RGD:2324990 NCBI chrNW_004936816:129,926...159,396 JBrowse link
G Muc5b mucin 5B, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chrNW_004936816:174,943...209,241 JBrowse link
G Muc6 mucin 6, oligomeric mucus/gel-forming ISO protein:increased expression: : RGD PMID:10209489 RGD:2325167 NCBI chrNW_004936816:882...14,717 JBrowse link
G Ncam1 neural cell adhesion molecule 1 ISO associated with hepatitis RGD PMID:12031086 RGD:2326079 NCBI chrNW_004936612:1,262,557...1,556,281 JBrowse link
G Nos2 nitric oxide synthase 2 ISO protein:increased expression:bile duct
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:16094703 PMID:16818635 RGD:2325280 NCBI chrNW_004936538:4,052,277...4,097,051 JBrowse link
G Notch1 notch receptor 1 ISO protein:increased expression:cholangiocyte RGD PMID:15887117 RGD:2325330 NCBI chrNW_004936669:1,292,016...1,334,061 JBrowse link
G Nr1h4 nuclear receptor subfamily 1 group H member 4 disease_progression ISO mRNA:decreased expression:liver (rat) RGD PMID:24255171 RGD:15090822 NCBI chrNW_004936492:13,315,265...13,365,186 JBrowse link
G Ogg1 8-oxoguanine DNA glycosylase disease_progression ISO DNA:loss of heterozygosity (human) RGD PMID:11260864 PMID:11866974 RGD:2317134 RGD:2317136 NCBI chrNW_004936602:3,411,106...3,418,826 JBrowse link
G Osbp2 oxysterol binding protein 2 ISO mRNA:increased expression:blood RGD PMID:21763455 RGD:41404644 NCBI chrNW_004936755:31,113...120,747 JBrowse link
G Osbpl7 oxysterol binding protein like 7 ISO mRNA:increased expression:blood RGD PMID:21763455 RGD:41404644 NCBI chrNW_004936490:13,491,704...13,506,742 JBrowse link
G Pawr pro-apoptotic WT1 regulator ISO mRNA,protein:decreased expression:cholangiocyte: RGD PMID:20724592 RGD:9835357 NCBI chrNW_004936698:650,225...746,593 JBrowse link
G Pbrm1 polybromo 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936473:3,382,618...3,476,049 JBrowse link
G Peg3 paternally expressed 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936882:577,424...607,691 JBrowse link
G Ppia peptidylprolyl isomerase A ameliorates ISO human cell line and construct in a mouse model RGD PMID:21871105 RGD:150429623 NCBI chrNW_004936478:19,669,727...19,673,355 JBrowse link
G Prkaca protein kinase cAMP-activated catalytic subunit alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936659:2,750,015...2,765,914 JBrowse link
G Prkacb protein kinase cAMP-activated catalytic subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936608:1,353,905...1,464,636 JBrowse link
G Pten phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:23376645 PMID:27022031 RGD:12802341 NCBI chrNW_004936735:1,252,414...1,338,318 JBrowse link
G Ptgs2 prostaglandin-endoperoxide synthase 2 ISO protein:increased expression:bile duct
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:16818635 PMID:19621664 RGD:2317180 NCBI chrNW_004936481:3,821,564...3,828,086 JBrowse link
G Reg1a regenerating family member 1 alpha susceptibility ISO mRNA, protein:increased expression:liver (human) RGD PMID:11343228 RGD:10044031 NCBI chrNW_004936556:4,873,331...4,875,608 JBrowse link
G Rnf43 ring finger protein 43 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936490:4,660,904...4,742,669 JBrowse link
G Robo2 roundabout guidance receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936505:5,544,011...6,747,417 JBrowse link
G Runx3 RUNX family transcription factor 3 ISO protein:decreased expression:bile duct RGD PMID:19827872 RGD:2324955 NCBI chrNW_004936474:9,751,946...9,802,910 JBrowse link
G Slc5a5 solute carrier family 5 member 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17408651 NCBI chrNW_004936596:3,176,009...3,188,637 JBrowse link
G Smad4 SMAD family member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936497:12,242,869...12,278,012 JBrowse link
G Sox17 SRY-box transcription factor 17 severity ISO RGD PMID:20816680 RGD:4889598 NCBI chrNW_004936496:1,248,582...1,251,406 JBrowse link
G Tgfb1 transforming growth factor beta 1 disease_progression ISO protein:increased expression:pancreas RGD PMID:12632524 PMID:16083599 RGD:1299231 RGD:2325020 NCBI chrNW_004936661:3,742,080...3,758,266 JBrowse link
G Tgfbr2 transforming growth factor beta receptor 2 ISO mRNA:increased expression:bile duct RGD PMID:12632524 RGD:1299231 NCBI chrNW_004936473:21,324,669...21,409,430 JBrowse link
G Thbs1 thrombospondin 1 disease_progression ISO DNA:hypermethylation (human) RGD PMID:11927969 PMID:12213730 PMID:16465407 RGD:2325024 RGD:2325026 RGD:2325027 NCBI chrNW_004936471:3,064,466...3,081,125 JBrowse link
G Tnc tenascin C severity ISO RGD PMID:20816680 RGD:4889598 NCBI chrNW_004936487:4,172,263...4,256,780 JBrowse link
G Tp53 tumor protein p53 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635 PMID:22561520 NCBI chrNW_004936595:919,807...935,367 JBrowse link
extrahepatic bile duct adenocarcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bap1 BRCA1 associated protein 1 disease_progression ISO RGD PMID:25536104 RGD:150340631 NCBI chrNW_004936473:3,239,009...3,247,806 JBrowse link
G Pbrm1 polybromo 1 disease_progression ISO RGD PMID:25536104 RGD:150340631 NCBI chrNW_004936473:3,382,618...3,476,049 JBrowse link
intrahepatic cholangiocarcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apc APC regulator of WNT signaling pathway ISO ClinVar Annotator: match by term: Intrahepatic Cholangiocarcinoma ClinVar PMID:24728327 PMID:25479140 PMID:25741868 PMID:26530882 PMID:28492532 NCBI chrNW_004936531:6,899,580...7,019,016 JBrowse link
G Arid1a AT-rich interaction domain 1A disease_progression
exacerbates
ISO protein:decreased expression:intrahepatic bile duct (human)
mRNA,protein:decreased expression:intrahepatic bile duct (human)
RGD PMID:27433094 PMID:30849962 PMID:31665232 RGD:126775257 RGD:126781775 RGD:14974231 NCBI chrNW_004936474:11,148,857...11,197,312 JBrowse link
G Bap1 BRCA1 associated protein 1 disease_progression ISO RGD PMID:27864835 RGD:150340628 NCBI chrNW_004936473:3,239,009...3,247,806 JBrowse link
G Becn1 beclin 1 disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chrNW_004936490:17,518,100...17,531,126 JBrowse link
G Braf B-Raf proto-oncogene, serine/threonine kinase severity ISO DNA:missense mutation:cds:p.V600E (human) RGD PMID:24139215 RGD:14398746 NCBI chrNW_004936592:4,728,371...4,833,830 JBrowse link
G Fas Fas cell surface death receptor disease_progression ISO RGD PMID:11003620 RGD:14700701 NCBI chrNW_004936735:209,369...234,582 JBrowse link
G Faslg Fas ligand severity ISO RGD PMID:11003620 RGD:14700701 NCBI chrNW_004936481:14,789,547...14,795,780 JBrowse link
G Foxp3 forkhead box P3 ISO DNA:hypomethylation:liver RGD PMID:24291052 RGD:38599002 NCBI chrNW_004936721:1,118,376...1,125,282 JBrowse link
G Idh1 isocitrate dehydrogenase (NADP(+)) 1 no_association ISO DNA:misssense mutations:cds:p.Arg132Cys,Arg132Leu (human) RGD PMID:26245674 RGD:14974229 NCBI chrNW_004936950:334,894...349,221 JBrowse link
G Idh2 isocitrate dehydrogenase (NADP(+)) 2 disease_progression ISO DNA:mutations: :
mRNA:decreased expression:liver (mouse)
RGD PMID:22824796 PMID:32463951 RGD:149735894 RGD:14985256 NCBI chrNW_004936483:15,845,777...15,864,341 JBrowse link
G Kras KRAS proto-oncogene, GTPase disease_progression ISO DNA:mutations:: RGD PMID:24139215 RGD:14398746 NCBI chrNW_004936548:2,078,568...2,113,877 JBrowse link
G Lcn2 lipocalin 2 treatment ISO Protein:increased expression:bile duct RGD PMID:24939880 RGD:126790491 NCBI chrNW_004936487:15,721,752...15,725,396 JBrowse link
G Lrp1b LDL receptor related protein 1B exacerbates ISO DNA:mutations:multiple: (human) RGD PMID:33014052 RGD:150429786 NCBI chrNW_004936469:35,000,773...36,160,216 JBrowse link
G Pbrm1 polybromo 1 ISO RGD PMID:27864835 RGD:150340628 NCBI chrNW_004936473:3,382,618...3,476,049 JBrowse link
G Smad4 SMAD family member 4 disease_progression ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 PMID:23981608 RGD:18936999 RGD:21066336 NCBI chrNW_004936497:12,242,869...12,278,012 JBrowse link
Klatskin's tumor term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apc APC regulator of WNT signaling pathway ISO ClinVar Annotator: match by term: Klatskin tumor ClinVar PMID:25741868 PMID:28492532 NCBI chrNW_004936531:6,899,580...7,019,016 JBrowse link
G Arid1a AT-rich interaction domain 1A disease_progression ISO DNA:deletions RGD PMID:33387086 RGD:126848756 NCBI chrNW_004936474:11,148,857...11,197,312 JBrowse link
G Gata6 GATA binding protein 6 sexual_dimorphism ISO DNA:mutations RGD PMID:33387086 RGD:126848756 NCBI chrNW_004936550:1,814,336...1,844,399 JBrowse link
G Kmt2c lysine methyltransferase 2C onset ISO DNA:mutations RGD PMID:33387086 RGD:126848756 NCBI chrNW_004936527:7,310,885...7,508,032 JBrowse link
G Kras KRAS proto-oncogene, GTPase disease_progression ISO DNA:mutations RGD PMID:33387086 RGD:126848756 NCBI chrNW_004936548:2,078,568...2,113,877 JBrowse link
G Prex2 phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 2 sexual_dimorphism ISO DNA:mutations RGD PMID:33387086 RGD:126848756 NCBI chrNW_004936496:6,005,410...6,284,332 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 13019
    disease of cellular proliferation 6279
      Neoplasms by Histologic Type 4292
        Glandular and Epithelial Neoplasms 3066
          carcinoma 2616
            bile duct carcinoma 78
              ampulla of Vater carcinoma + 0
              bile duct adenocarcinoma + 78
              bile duct carcinoma in situ 0
              bile duct mucoepidermoid carcinoma 0
              distal biliary tract carcinoma 0
              squamous cell bile duct carcinoma + 0
Path 2
Term Annotations click to browse term
  disease 13019
    disease of anatomical entity 12700
      gastrointestinal system disease 5142
        Digestive System Neoplasms 3126
          Gastrointestinal Neoplasms 3015
            gastrointestinal system benign neoplasm 149
              hepatobiliary benign neoplasm 118
                biliary tract benign neoplasm 92
                  Bile Duct Neoplasms 90
                    bile duct cancer 88
                      bile duct carcinoma 78
                        ampulla of Vater carcinoma + 0
                        bile duct adenocarcinoma + 78
                        bile duct carcinoma in situ 0
                        bile duct mucoepidermoid carcinoma 0
                        distal biliary tract carcinoma 0
                        squamous cell bile duct carcinoma + 0
paths to the root