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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:hepatobiliary benign neoplasm
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Accession:DOID:3117 term browser browse the term
Definition:A gastrointestinal system benign neoplasm located_in the hepatobiliary system. (DO)
Synonyms:exact_synonym: hepatobiliary tumors
 primary_id: RDO:9004093
 xref: NCI:C8614
For additional species annotation, visit the Alliance of Genome Resources.


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bile duct adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Braf Braf transforming gene IAGP DNA:missense mutation:cds:p.V600E (human) RGD PMID:25704541 RGD:11521169 NCBI chr 6:39,603,231...39,725,658
Ensembl chr 6:39,603,237...39,725,463
JBrowse link
bile duct cancer term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apob apolipoprotein B susceptibility ISO DNA:polymorphisms:intron, exon:IVS6+360C>T, 56C>T (human) RGD PMID:18296645 RGD:2317550 NCBI chr12:7,977,629...8,016,839
Ensembl chr12:7,977,648...8,016,835
JBrowse link
G Apoe apolipoprotein E susceptibility ISO DNA:SNP:intron:rs440446 (human) RGD PMID:18296645 RGD:2317550 NCBI chr 7:19,696,244...19,701,310
Ensembl chr 7:19,696,109...19,699,188
JBrowse link
G Tjp1 tight junction protein 1 ISO protein:decreased expression:bile duct RGD PMID:19184677 RGD:2325030 NCBI chr 7:65,296,165...65,527,850
Ensembl chr 7:65,296,165...65,527,781
JBrowse link
bile duct carcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Msln mesothelin ISO protein:increased expression:bile duct RGD PMID:17276942 RGD:2326059 NCBI chr17:25,748,613...25,754,378
Ensembl chr17:25,748,613...25,754,378
JBrowse link
Bile Duct Neoplasms term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Asph aspartate-beta-hydroxylase ISO mRNA:increased expression:bile duct RGD PMID:16673309 RGD:2325824 NCBI chr 4:9,449,085...9,669,344
Ensembl chr 4:9,448,069...9,669,344
JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chr11:16,752,203...16,913,907
Ensembl chr11:16,752,203...16,918,158
JBrowse link
G Fscn1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile duct RGD PMID:17419223 RGD:2317786 NCBI chr 5:142,960,355...142,973,189
Ensembl chr 5:142,960,343...142,973,185
JBrowse link
G Il6 interleukin 6 disease_progression ISO protein:increased expression:serum RGD PMID:17617204 RGD:2317166 NCBI chr 5:30,013,114...30,019,975
Ensembl chr 5:30,013,114...30,019,981
JBrowse link
G Met met proto-oncogene ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15892172 RGD:2317585 NCBI chr 6:17,463,349...17,573,980
Ensembl chr 6:17,463,800...17,573,980
JBrowse link
G Mgmt O-6-methylguanine-DNA methyltransferase severity ISO protein:decreased expression:carcinoma of extrahepatic bile duct (human) RGD PMID:11986189 RGD:2317662 NCBI chr 7:136,894,463...137,128,193
Ensembl chr 7:136,894,614...137,130,266
JBrowse link
G Mki67 antigen identified by monoclonal antibody Ki 67 disease_progression ISO RGD PMID:9869516 RGD:2317706 NCBI chr 7:135,689,784...135,716,450
Ensembl chr 7:135,689,784...135,716,361
JBrowse link
G Muc16 mucin 16 ISO protein:increased expression:serum,bile RGD PMID:1657243 RGD:2325134 NCBI chr 9:18,495,445...18,674,821
Ensembl chr 9:18,495,455...18,674,530
JBrowse link
G Muc4 mucin 4 disease_progression ISO protein:increased expression:bile duct RGD PMID:16857800 RGD:2324929 NCBI chr16:32,735,886...32,782,391
Ensembl chr16:32,735,886...32,782,391
JBrowse link
G Ncam1 neural cell adhesion molecule 1 disease_progression ISO RGD PMID:8501910, PMID:9851639 RGD:2326077, RGD:2326076 NCBI chr 9:49,502,129...49,799,393
Ensembl chr 9:49,502,136...49,798,925
JBrowse link
G Runx3 runt related transcription factor 3 ISO DNA:hypermethylation:promoter RGD PMID:15471559 RGD:2324957 NCBI chr 4:135,120,645...135,177,990
Ensembl chr 4:135,120,652...135,177,990
JBrowse link
biliary tract benign neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Alb albumin disease_progression ISO RGD PMID:20358256 RGD:2325676 NCBI chr 5:90,460,870...90,476,602
Ensembl chr 5:90,460,897...90,476,602
JBrowse link
G Ctps cytidine 5'-triphosphate synthase ISO mRNA:increased expression:biliary tract neoplasm (human) RGD PMID:12819026 RGD:2317903 NCBI chr 4:120,539,868...120,570,276
Ensembl chr 4:120,539,868...120,570,276
JBrowse link
G Elf3 E74-like factor 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 1:135,253,574...135,258,472
Ensembl chr 1:135,253,575...135,258,568
JBrowse link
G Fasl Fas ligand (TNF superfamily, member 6) ISO protein:decreased expression:serum
associated with Biliary Tract Disease;protein:decreased expression:serum
RGD PMID:15138553, PMID:15287856 RGD:2317743, RGD:2317742 NCBI chr 1:161,780,691...161,788,495
Ensembl chr 1:161,780,689...161,788,495
JBrowse link
G Hgf hepatocyte growth factor ISO mRNA:increased expression: : RGD PMID:12819026 RGD:2317903 NCBI chr 5:16,553,495...16,619,439
Ensembl chr 5:16,553,495...16,620,152
JBrowse link
G Il4 interleukin 4 ISO RGD PMID:18798553 RGD:2317263 NCBI chr11:53,612,460...53,618,665
Ensembl chr11:53,602,982...53,618,669
JBrowse link
G Il6 interleukin 6 ISO RGD PMID:18159174 RGD:2317165 NCBI chr 5:30,013,114...30,019,975
Ensembl chr 5:30,013,114...30,019,981
JBrowse link
G Mdm2 transformed mouse 3T3 cell double minute 2 ISO protein:increased expression:biliary epithelium (human) RGD PMID:16505435 RGD:2317415 NCBI chr10:117,688,875...117,710,758
Ensembl chr10:117,688,875...117,710,758
JBrowse link
G Mtap methylthioadenosine phosphorylase ISO RGD PMID:16373701 RGD:2317953 NCBI chr 4:89,137,370...89,181,090
Ensembl chr 4:89,137,122...89,181,081
JBrowse link
G Muc1 mucin 1, transmembrane ISO RGD PMID:19129927 RGD:2317987 NCBI chr 3:89,229,056...89,233,381
Ensembl chr 3:89,229,057...89,233,381
JBrowse link
G Muc4 mucin 4 ISO protein:increased expression:bile,biliary tract RGD PMID:18475301 RGD:2324916 NCBI chr16:32,735,886...32,782,391
Ensembl chr16:32,735,886...32,782,391
JBrowse link
G Muc5ac mucin 5, subtypes A and C, tracheobronchial/gastric disease_progression ISO protein:increased expression:serum RGD PMID:18475301 RGD:2324916 NCBI chr 7:141,788,958...141,819,227
Ensembl chr 7:141,788,972...141,819,231
JBrowse link
G Prkacb protein kinase, cAMP dependent, catalytic, beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 3:146,729,579...146,812,946
Ensembl chr 3:146,729,574...146,812,990
JBrowse link
cholangiocarcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcc2 ATP-binding cassette, sub-family C (CFTR/MRP), member 2 susceptibility ISO DNA:polymorphism:exon:c.3972C>T (human) RGD PMID:19451719 RGD:2317508 NCBI chr19:43,782,308...43,838,332
Ensembl chr19:43,782,192...43,840,740
JBrowse link
G Adrb2 adrenergic receptor, beta 2 ISO protein:decreased expression:liver RGD PMID:16292515 RGD:2325640 NCBI chr18:62,177,713...62,179,981
Ensembl chr18:62,177,816...62,179,959
JBrowse link
G Alb albumin disease_progression ISO RGD PMID:10776430, PMID:20431764, PMID:17545000 RGD:2325682, RGD:2325679, RGD:2325680 NCBI chr 5:90,460,870...90,476,602
Ensembl chr 5:90,460,897...90,476,602
JBrowse link
G Alox5 arachidonate 5-lipoxygenase ISO protein:increased expression:bile duct RGD PMID:18507031 RGD:2317521 NCBI chr 6:116,410,071...116,461,178
Ensembl chr 6:116,410,077...116,461,178
JBrowse link
G Anxa2 annexin A2 disease_progression ISO RGD PMID:20493868 RGD:2325728 NCBI chr 9:69,453,683...69,491,792
Ensembl chr 9:69,453,620...69,491,795
JBrowse link
G Anxa8 annexin A8 ISO RGD PMID:19376120 RGD:2325733 NCBI chr14:34,085,979...34,100,571
Ensembl chr14:34,085,981...34,100,571
JBrowse link
G Apc APC, WNT signaling pathway regulator ISO DNA:hypermethylation:promoter
DNA:loss of heterozygosity
RGD PMID:15467712, PMID:10212000 RGD:2317198, RGD:2317205 NCBI chr18:34,220,297...34,322,190
Ensembl chr18:34,220,924...34,322,552
JBrowse link
G Apoa1 apolipoprotein A-I ISO protein:decreased expression:serum RGD PMID:19486127 RGD:2325756 NCBI chr 9:46,228,630...46,230,469
Ensembl chr 9:46,228,580...46,230,466
JBrowse link
G Arid1a AT rich interactive domain 1A (SWI-like) ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr 4:133,679,008...133,756,769
Ensembl chr 4:133,679,008...133,756,769
JBrowse link
G Asph aspartate-beta-hydroxylase ISO RGD PMID:21898484 RGD:6902945 NCBI chr 4:9,449,085...9,669,344
Ensembl chr 4:9,448,069...9,669,344
JBrowse link
G Bap1 Brca1 associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509, PMID:25231345 NCBI chr14:31,251,352...31,259,930
Ensembl chr14:31,251,450...31,259,944
JBrowse link
G Braf Braf transforming gene IAGP DNA:missense mutation:cds:p.V600E (human) RGD PMID:12692057 RGD:11073239 NCBI chr 6:39,603,231...39,725,658
Ensembl chr 6:39,603,237...39,725,463
JBrowse link
G Cdkn2a cyclin dependent kinase inhibitor 2A onset ISO protein:decreased expression:liver RGD PMID:15619210 RGD:2317417 NCBI chr 4:89,274,473...89,294,619
Ensembl chr 4:89,274,471...89,294,653
JBrowse link
G Cycs cytochrome c, somatic ISO RGD PMID:19788692 RGD:2317615 NCBI chr 6:50,562,563...50,566,569
Ensembl chr 6:50,562,563...50,566,538
JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chr11:16,752,203...16,913,907
Ensembl chr11:16,752,203...16,918,158
JBrowse link
G Epo erythropoietin ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chr 5:137,483,020...137,485,816
Ensembl chr 5:137,483,020...137,533,242
JBrowse link
G Epor erythropoietin receptor ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chr 9:21,958,897...21,963,576
Ensembl chr 9:21,958,897...21,963,506
JBrowse link
G Erbb2 erb-b2 receptor tyrosine kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635 NCBI chr11:98,412,484...98,437,716
Ensembl chr11:98,412,470...98,437,716
JBrowse link
G Fasl Fas ligand (TNF superfamily, member 6) ISO RGD PMID:11029528 RGD:2317746 NCBI chr 1:161,780,691...161,788,495
Ensembl chr 1:161,780,689...161,788,495
JBrowse link
G Fgf2 fibroblast growth factor 2 ISO protein:increased expression:bile RGD PMID:11478488 RGD:2317765 NCBI chr 3:37,348,477...37,410,106
Ensembl chr 3:37,348,346...37,410,108
JBrowse link
G Fgfr2 fibroblast growth factor receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 7:130,162,451...130,266,808
Ensembl chr 7:130,162,451...133,123,350
JBrowse link
G Fscn1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile ducts RGD PMID:19721413 RGD:2317780 NCBI chr 5:142,960,355...142,973,189
Ensembl chr 5:142,960,343...142,973,185
JBrowse link
G Gnas GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus disease_progression ISO DNA:polymorphism:393T>C (human)
CTD Direct Evidence: marker/mechanism
CTD PMID:22561520, PMID:17356712 RGD:1601377 NCBI chr 2:174,284,320...174,346,744
Ensembl chr 2:174,284,320...174,346,744
JBrowse link
G Gstm1 glutathione S-transferase, mu 1 ISO RGD PMID:24049014 RGD:14700980 NCBI chr 3:108,012,250...108,017,973
Ensembl chr 3:108,012,255...108,017,973
JBrowse link
G Gstp1 glutathione S-transferase, pi 1 treatment ISO DNA:hypermethylation:promoter
human cell line in a mouse model
RGD PMID:15467712, PMID:12805482 RGD:2317198, RGD:14401711 NCBI chr19:4,035,411...4,037,912
Ensembl chr19:4,035,407...4,037,985
JBrowse link
G Hdac6 histone deacetylase 6 ISO protein:increased expression:liver: RGD PMID:23370327 RGD:9681560 NCBI chr  X:7,930,116...7,948,047
Ensembl chr  X:7,930,120...7,947,889
JBrowse link
G Hgf hepatocyte growth factor ISO mRNA, protein:increased expression: :
protein:increased expression:serum
RGD PMID:10827151, PMID:16974053 RGD:2317925, RGD:2317909 NCBI chr 5:16,553,495...16,619,439
Ensembl chr 5:16,553,495...16,620,152
JBrowse link
G Idh1 isocitrate dehydrogenase 1 (NADP+), soluble ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr 1:65,158,616...65,186,479
Ensembl chr 1:65,158,616...65,186,500
JBrowse link
G Idh2 isocitrate dehydrogenase 2 (NADP+), mitochondrial ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr 7:80,094,845...80,118,608
Ensembl chr 7:80,094,846...80,115,392
JBrowse link
G Il4ra interleukin 4 receptor, alpha ISO mRNA:increased expression:bile duct RGD PMID:18798553 RGD:2317263 NCBI chr 7:125,552,271...125,579,474
Ensembl chr 7:125,552,120...125,579,474
JBrowse link
G Il6 interleukin 6 ISO protein:increased expression:serum
CTD Direct Evidence: marker/mechanism
CTD PMID:17621267, PMID:15011822, PMID:28925763 RGD:2317167, RGD:14975292 NCBI chr 5:30,013,114...30,019,975
Ensembl chr 5:30,013,114...30,019,981
JBrowse link
G Kmt2c lysine (K)-specific methyltransferase 2C ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr 5:25,271,795...25,498,855
Ensembl chr 5:25,271,798...25,498,783
JBrowse link
G Kras Kirsten rat sarcoma viral oncogene homolog ISO CTD Direct Evidence: marker/mechanism CTD PMID:8968066, PMID:22561520 NCBI chr 6:145,216,699...145,250,420
Ensembl chr 6:145,216,699...145,250,239
JBrowse link
G Krt7 keratin 7 ISO RGD PMID:18393293 RGD:2317308 NCBI chr15:101,412,403...101,427,806
Ensembl chr15:101,411,043...101,430,313
JBrowse link
G Mdm2 transformed mouse 3T3 cell double minute 2 disease_progression ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15619210 RGD:2317417 NCBI chr10:117,688,875...117,710,758
Ensembl chr10:117,688,875...117,710,758
JBrowse link
G Met met proto-oncogene disease_progression ISO protein:increased phosphorylation:liver, carcinoma (human)
protein:increased expression:liver, biliary epithelium (rat)
RGD PMID:16818635, PMID:14656942 RGD:2317578, RGD:2317601 NCBI chr 6:17,463,349...17,573,980
Ensembl chr 6:17,463,800...17,573,980
JBrowse link
G Mgmt O-6-methylguanine-DNA methyltransferase ISO DNA:hypermethylation:promoter (human) RGD PMID:17550320 RGD:2317632 NCBI chr 7:136,894,463...137,128,193
Ensembl chr 7:136,894,614...137,130,266
JBrowse link
G Mir155 microRNA 155 ISO miRNA:increased expression:serum RGD PMID:30653586 RGD:21081530 NCBI chr16:84,714,140...84,714,204
Ensembl chr16:84,714,140...84,714,204
JBrowse link
G Mki67 antigen identified by monoclonal antibody Ki 67 disease_progression ISO RGD PMID:12903495 RGD:2317705 NCBI chr 7:135,689,784...135,716,450
Ensembl chr 7:135,689,784...135,716,361
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 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 mRNA:increased expression:bile duct
protein:increased expression:bile duct
RGD PMID:16463672, PMID:15213623, PMID:15213623 RGD:2325856, RGD:2324667, RGD:2324667 NCBI chr 2:164,940,326...164,955,850
Ensembl chr 2:164,940,780...164,955,850
JBrowse link
G Msln mesothelin ISO CTD Direct Evidence: marker/mechanism CTD PMID:14576474 NCBI chr17:25,748,613...25,754,378
Ensembl chr17:25,748,613...25,754,378
JBrowse link
G Mthfr methylenetetrahydrofolate reductase susceptibility ISO DNA:polymorphism (human) RGD PMID:17201138 RGD:2317119 NCBI chr 4:148,039,077...148,059,562
Ensembl chr 4:148,039,077...148,059,551
JBrowse link
G Muc1 mucin 1, transmembrane disease_progression ISO protein:increased secretion:bile
mRNA:increased expression:bile duct
protein:increased expression:bile duct:
protein:increased expression:serum
RGD PMID:19055478, PMID:18081149, PMID:15213623, PMID:19260467, PMID:19639217 RGD:2324622, RGD:2324638, RGD:2324667, RGD:2324664, RGD:2317986 NCBI chr 3:89,229,056...89,233,381
Ensembl chr 3:89,229,057...89,233,381
JBrowse link
G Muc16 mucin 16 ISO associated with Opisthorchiasis;protein:increased expression:serum RGD PMID:1653472 RGD:2325142 NCBI chr 9:18,495,445...18,674,821
Ensembl chr 9:18,495,455...18,674,530
JBrowse link
G Muc2 mucin 2 ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chr 7:141,690,340...141,754,691
Ensembl chr 7:141,690,340...141,754,693
JBrowse link
G Muc3a mucin 3A, cell surface associated ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chr 5:137,208,805...137,212,545
Ensembl chr 5:137,208,813...137,212,389
JBrowse link
G Muc4 mucin 4 disease_progression ISO protein:increased expression:bile duct RGD PMID:14752841, PMID:19082442 RGD:2324944, RGD:2303602 NCBI chr16:32,735,886...32,782,391
Ensembl chr16:32,735,886...32,782,391
JBrowse link
G Muc5ac mucin 5, subtypes A and C, tracheobronchial/gastric disease_progression ISO mRNA:increased expression:bile duct
protein:increased expression:serum
RGD PMID:11680592, PMID:14508831 RGD:2324948, RGD:2324990 NCBI chr 7:141,788,958...141,819,227
Ensembl chr 7:141,788,972...141,819,231
JBrowse link
G Muc5b mucin 5, subtype B, tracheobronchial ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chr 7:141,839,059...141,873,089
Ensembl chr 7:141,839,070...141,873,084
JBrowse link
G Muc6 mucin 6, gastric ISO protein:increased expression: : RGD PMID:10209489 RGD:2325167 NCBI chr 7:141,633,459...141,655,393
Ensembl chr 7:141,633,456...141,655,319
JBrowse link
G Nat2 N-acetyltransferase 2 (arylamine N-acetyltransferase) ISO DNA:polymorphisms (human) RGD PMID:15901993 RGD:2317172 NCBI chr 8:67,494,875...67,502,644
Ensembl chr 8:67,494,858...67,502,584
JBrowse link
G Ncam1 neural cell adhesion molecule 1 ISO associated with hepatitis RGD PMID:12031086 RGD:2326079 NCBI chr 9:49,502,129...49,799,393
Ensembl chr 9:49,502,136...49,798,925
JBrowse link
G Nos2 nitric oxide synthase 2, inducible ISO protein:increased expression:bile duct
CTD Direct Evidence: marker/mechanism
CTD PMID:16818635, PMID:16094703 RGD:2325280 NCBI chr11:78,920,787...78,960,226
Ensembl chr11:78,920,787...78,960,254
JBrowse link
G Notch1 notch 1 ISO protein:increased expression:cholangiocyte RGD PMID:15887117 RGD:2325330 NCBI chr 2:26,457,902...26,503,822
Ensembl chr 2:26,457,903...26,516,663
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 chr10:89,454,234...89,533,645
Ensembl chr10:89,454,234...89,533,585
JBrowse link
G Ogg1 8-oxoguanine DNA-glycosylase 1 disease_progression ISO DNA:loss of heterozygosity (human) RGD PMID:11866974, PMID:11260864 RGD:2317134, RGD:2317136 NCBI chr 6:113,326,972...113,334,877
Ensembl chr 6:113,326,972...113,335,068
JBrowse link
G Pawr PRKC, apoptosis, WT1, regulator ISO mRNA,protein:decreased expression:cholangiocyte: RGD PMID:20724592 RGD:9835357 NCBI chr10:108,332,189...108,414,391
Ensembl chr10:108,332,121...108,414,240
JBrowse link
G Pbrm1 polybromo 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr14:31,019,138...31,121,592
Ensembl chr14:31,019,138...31,121,592
JBrowse link
G Peg3 paternally expressed 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr 7:6,703,892...6,730,462
Ensembl chr 7:6,703,892...6,730,431
JBrowse link
G Prkaca protein kinase, cAMP dependent, catalytic, alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 8:83,972,978...83,996,444
Ensembl chr 8:83,972,993...83,996,443
JBrowse link
G Prkacb protein kinase, cAMP dependent, catalytic, beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 3:146,729,579...146,812,946
Ensembl chr 3:146,729,574...146,812,990
JBrowse link
G Prss2 protease, serine 2 ISO protein:increased expression:serum RGD PMID:8621252 RGD:2324908 NCBI chr 6:41,521,776...41,525,079
Ensembl chr 6:41,521,787...41,525,079
JBrowse link
G Pten phosphatase and tensin homolog ISO
IMP
CTD Direct Evidence: marker/mechanism CTD PMID:27022031, PMID:23376645 RGD:12802341 NCBI chr19:32,757,577...32,826,160
Ensembl chr19:32,757,497...32,826,160
JBrowse link
G Ptgs2 prostaglandin-endoperoxide synthase 2 ISO protein:increased expression:bile duct
CTD Direct Evidence: marker/mechanism
CTD PMID:16818635, PMID:19621664 RGD:2317180 NCBI chr 1:150,100,031...150,108,234
Ensembl chr 1:150,100,031...150,108,227
JBrowse link
G Reg1 regenerating islet-derived 1 susceptibility ISO mRNA, protein:increased expression:liver (human) RGD PMID:11343228 RGD:10044031 NCBI chr 6:78,425,983...78,428,668
Ensembl chr 6:78,422,711...78,428,667
JBrowse link
G Rnf43 ring finger protein 43 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr11:87,663,087...87,735,539
Ensembl chr11:87,662,722...87,735,539
JBrowse link
G Robo2 roundabout guidance receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr16:73,891,976...75,447,443
Ensembl chr16:73,891,839...74,411,825
JBrowse link
G Runx3 runt related transcription factor 3 ISO protein:decreased expression:bile duct RGD PMID:19827872 RGD:2324955 NCBI chr 4:135,120,645...135,177,990
Ensembl chr 4:135,120,652...135,177,990
JBrowse link
G Slc5a5 solute carrier family 5 (sodium iodide symporter), member 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17408651 NCBI chr 8:70,882,885...70,892,785
Ensembl chr 8:70,882,889...70,892,757
JBrowse link
G Smad4 SMAD family member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr18:73,634,790...73,703,791
Ensembl chr18:73,639,009...73,703,780
JBrowse link
G Sox17 SRY (sex determining region Y)-box 17 severity ISO RGD PMID:20816680 RGD:4889598 NCBI chr 1:4,490,928...4,497,426
Ensembl chr 1:4,490,931...4,497,354
JBrowse link
G Tgfb1 transforming growth factor, beta 1 disease_progression ISO protein:increased expression:pancreas RGD PMID:16083599, PMID:12632524 RGD:2325020, RGD:1299231 NCBI chr 7:25,687,002...25,705,077
Ensembl chr 7:25,687,002...25,705,077
JBrowse link
G Tgfbr2 transforming growth factor, beta receptor II ISO mRNA:increased expression:bile duct RGD PMID:12632524 RGD:1299231 NCBI chr 9:116,087,695...116,175,363
Ensembl chr 9:116,084,293...116,175,360
JBrowse link
G Thbs1 thrombospondin 1 disease_progression ISO DNA:hypermethylation (human) RGD PMID:11927969, PMID:12213730, PMID:16465407 RGD:2325027, RGD:2325026, RGD:2325024 NCBI chr 2:118,111,876...118,127,133
Ensembl chr 2:118,111,876...118,127,133
JBrowse link
G Tnc tenascin C severity ISO RGD PMID:20816680 RGD:4889598 NCBI chr 4:63,959,785...64,047,015
Ensembl chr 4:63,959,785...64,047,015
JBrowse link
G Trp53 transformation related protein 53 ISO
EXP
CTD Direct Evidence: marker/mechanism CTD PMID:16818635, PMID:22561520 NCBI chr11:69,580,348...69,591,873
Ensembl chr11:69,580,359...69,591,873
JBrowse link
G Ugt1a9 UDP glucuronosyltransferase 1 family, polypeptide A9 ISO RGD PMID:9230212 RGD:2325161 NCBI chr 1:88,070,779...88,220,002
Ensembl chr 1:88,070,800...88,218,997
JBrowse link
common bile duct neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apob apolipoprotein B ISO protein:increased expression:serum RGD PMID:18076041 RGD:2325763 NCBI chr12:7,977,629...8,016,839
Ensembl chr12:7,977,648...8,016,835
JBrowse link
G Fscn1 fascin actin-bundling protein 1 ISO mRNA, protein:increased expression: : RGD PMID:15136764 RGD:2317789 NCBI chr 5:142,960,355...142,973,189
Ensembl chr 5:142,960,343...142,973,185
JBrowse link
G Msln mesothelin ISO protein:increased expression:common bile duct, ampulla of vater RGD PMID:16416732 RGD:2326064 NCBI chr17:25,748,613...25,754,378
Ensembl chr17:25,748,613...25,754,378
JBrowse link
G Mtap methylthioadenosine phosphorylase ISO DNA, protein:deletion, decreased expression:common bile duct: RGD PMID:15662124 RGD:2317954 NCBI chr 4:89,137,370...89,181,090
Ensembl chr 4:89,137,122...89,181,081
JBrowse link
G Muc1 mucin 1, transmembrane disease_progression ISO protein:increased expression:bile duct RGD PMID:8766528 RGD:2324856 NCBI chr 3:89,229,056...89,233,381
Ensembl chr 3:89,229,057...89,233,381
JBrowse link
G Muc4 mucin 4 ISO protein:increased expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chr16:32,735,886...32,782,391
Ensembl chr16:32,735,886...32,782,391
JBrowse link
G Muc5ac mucin 5, subtypes A and C, tracheobronchial/gastric ISO protein:altered expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chr 7:141,788,958...141,819,227
Ensembl chr 7:141,788,972...141,819,231
JBrowse link
G Tymp thymidine phosphorylase disease_progression ISO RGD PMID:10760693 RGD:2325158 NCBI chr15:89,371,631...89,377,036
Ensembl chr15:89,371,931...89,377,039
JBrowse link
familial hepatic adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hnf1a HNF1 homeobox A ISO ClinVar Annotator: match by term: Hepatic adenomas, familial ClinVar
OMIM
PMID:8866553, PMID:8945470, PMID:9032114, PMID:9045858, PMID:9075818, PMID:9166684, PMID:9313763, PMID:9392505, PMID:9439666, PMID:10333057, PMID:10447526, PMID:10754480, PMID:11058894, PMID:11315851, PMID:12050210, PMID:12355088, PMID:12530534, PMID:12574234, PMID:12618559, PMID:15649945, PMID:15928245, PMID:17054605, PMID:17407387, PMID:17440016, PMID:17573900, PMID:17937063, PMID:17989309, PMID:18414213, PMID:18672310, PMID:21051477, PMID:21628466, PMID:23551881, PMID:23607861, PMID:25174781, PMID:26467025 NCBI chr 5:114,948,980...114,971,062
Ensembl chr 5:114,948,980...114,971,094
JBrowse link
hepatic angiomyolipoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tsc2 TSC complex subunit 2 IAGP DNA:mutations:multiple
associated with tuberous sclerosis;DNA:mutations:multiple
RGD PMID:29512829, PMID:22251200 RGD:21079730, RGD:21079732 NCBI chr17:24,595,816...24,632,676
Ensembl chr17:24,595,816...24,632,630
JBrowse link
hepatocellular adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G A2m alpha-2-macroglobulin ISO mRNA,protein:increased expression:liver:
CTD Direct Evidence: marker/mechanism
CTD PMID:15509519, PMID:15509519 RGD:1358261 NCBI chr 6:121,636,165...121,679,238
Ensembl chr 6:121,635,376...121,679,227
JBrowse link
G Carm1 coactivator-associated arginine methyltransferase 1 ISO mRNA,protein:increased expression:liver: RGD PMID:23912631 RGD:9586718 NCBI chr 9:21,546,894...21,589,467
Ensembl chr 9:21,546,894...21,592,623
JBrowse link
G Cdkn1b cyclin-dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:17620307 NCBI chr 6:134,920,401...134,925,525
Ensembl chr 6:134,920,401...134,925,513
JBrowse link
G Ctnnb1 catenin (cadherin associated protein), beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21147764 NCBI chr 9:120,933,400...120,960,507
Ensembl chr 9:120,929,216...120,960,507
JBrowse link
G Cyp2e1 cytochrome P450, family 2, subfamily e, polypeptide 1 treatment ISO RGD PMID:23543859 RGD:14700918 NCBI chr 7:140,763,819...140,774,990
Ensembl chr 7:140,763,739...140,774,987
JBrowse link
G Hnf1a HNF1 homeobox A susceptibility IAGP DNA:loss of heterozygosity, mutations:multiple
DNA:frameshift mutation, non-sense mutation:cds:R229X, G55fsX57 (human)
RGD PMID:12355088, PMID:14598263 RGD:14700683, RGD:14700774 NCBI chr 5:114,948,980...114,971,062
Ensembl chr 5:114,948,980...114,971,094
JBrowse link
G Hp haptoglobin ISO RGD PMID:10569800 RGD:1626391 NCBI chr 8:109,575,128...109,579,172
Ensembl chr 8:109,575,128...109,579,172
JBrowse link
G Hras Harvey rat sarcoma virus oncogene ISO CTD Direct Evidence: marker/mechanism CTD PMID:8200073 NCBI chr 7:141,189,934...141,194,019
Ensembl chr 7:141,189,105...141,194,005
JBrowse link
G Kras Kirsten rat sarcoma viral oncogene homolog induced ISO aflatoxin B1 induced:DNA:transversion,transition mutations:cds: RGD PMID:8446626 RGD:11568697 NCBI chr 6:145,216,699...145,250,420
Ensembl chr 6:145,216,699...145,250,239
JBrowse link
G Mki67 antigen identified by monoclonal antibody Ki 67 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31939706 NCBI chr 7:135,689,784...135,716,450
Ensembl chr 7:135,689,784...135,716,361
JBrowse link
G Nr1h4 nuclear receptor subfamily 1, group H, member 4 IMP RGD PMID:17183066 RGD:14696794 NCBI chr10:89,454,234...89,533,645
Ensembl chr10:89,454,234...89,533,585
JBrowse link
G Nr1i3 nuclear receptor subfamily 1, group I, member 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25656644 NCBI chr 1:171,213,934...171,218,845
Ensembl chr 1:171,213,970...171,220,701
JBrowse link
G Pten phosphatase and tensin homolog IMP
ISO
CTD Direct Evidence: marker/mechanism CTD PMID:27022031, PMID:15199412 RGD:1302555 NCBI chr19:32,757,577...32,826,160
Ensembl chr19:32,757,497...32,826,160
JBrowse link
G Ptpn11 protein tyrosine phosphatase, non-receptor type 11 IEA MouseDO NCBI chr 5:121,130,533...121,191,397
Ensembl chr 5:121,130,533...121,191,397
JBrowse link
G Tmem70 transmembrane protein 70 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr 1:16,665,191...16,678,275
Ensembl chr 1:16,665,207...16,678,275
JBrowse link
G Ube2e2 ubiquitin-conjugating enzyme E2E 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr14:18,573,563...18,894,284
Ensembl chr14:18,573,575...18,894,267
JBrowse link
intrahepatic cholangiocarcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apc APC, WNT signaling pathway regulator ISO ClinVar Annotator: match by term: Intrahepatic Cholangiocarcinoma ClinVar PMID:24728327, PMID:25479140, PMID:25741868, PMID:26530882, PMID:28492532 NCBI chr18:34,220,297...34,322,190
Ensembl chr18:34,220,924...34,322,552
JBrowse link
G Arid1a AT rich interactive domain 1A (SWI-like) disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chr 4:133,679,008...133,756,769
Ensembl chr 4:133,679,008...133,756,769
JBrowse link
G Becn1 beclin 1, autophagy related disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chr11:101,288,258...101,302,286
Ensembl chr11:101,285,952...101,302,286
JBrowse link
G Braf Braf transforming gene severity IAGP DNA:missense mutation:cds:p.V600E (human) RGD PMID:24139215 RGD:14398746 NCBI chr 6:39,603,231...39,725,658
Ensembl chr 6:39,603,237...39,725,463
JBrowse link
G Fas Fas (TNF receptor superfamily member 6) disease_progression ISO RGD PMID:11003620 RGD:14700701 NCBI chr19:34,290,647...34,327,775
Ensembl chr19:34,290,666...34,327,772
JBrowse link
G Fasl Fas ligand (TNF superfamily, member 6) severity ISO RGD PMID:11003620 RGD:14700701 NCBI chr 1:161,780,691...161,788,495
Ensembl chr 1:161,780,689...161,788,495
JBrowse link
G Foxp3 forkhead box P3 ISO DNA:hypomethylation:liver RGD PMID:24291052 RGD:38599002 NCBI chr  X:7,579,676...7,595,243
Ensembl chr  X:7,573,644...7,595,245
JBrowse link
G Idh1 isocitrate dehydrogenase 1 (NADP+), soluble no_association ISO DNA:misssense mutations:cds:p.Arg132Cys,Arg132Leu (human) RGD PMID:26245674 RGD:14974229 NCBI chr 1:65,158,616...65,186,479
Ensembl chr 1:65,158,616...65,186,500
JBrowse link
G Idh2 isocitrate dehydrogenase 2 (NADP+), mitochondrial disease_progression ISO DNA:mutations: : RGD PMID:22824796 RGD:14985256 NCBI chr 7:80,094,845...80,118,608
Ensembl chr 7:80,094,846...80,115,392
JBrowse link
G Kras Kirsten rat sarcoma viral oncogene homolog disease_progression IEA
ISO
DNA:mutations:: MouseDO PMID:24139215 RGD:14398746 NCBI chr 6:145,216,699...145,250,420
Ensembl chr 6:145,216,699...145,250,239
JBrowse link
G Mir152 microRNA 152 ISO miRNA:decreased expression:intrahepatic bile duct RGD PMID:28921383 RGD:19165148 NCBI chr11:96,850,393...96,850,465
Ensembl chr11:96,850,393...96,850,465
JBrowse link
G Mir200b microRNA 200b ISO RNA:increased expression:liver RGD PMID:27685844 RGD:14928335 NCBI chr 4:156,055,681...156,055,750
Ensembl chr 4:156,055,681...156,055,750
JBrowse link
G Mir21a microRNA 21a ISO RNA:increased expression:liver,plasma RGD PMID:27685844 RGD:14928335 NCBI chr11:86,584,067...86,584,158
Ensembl chr11:86,584,067...86,584,158
JBrowse link
G Mir221 microRNA 221 severity ISO RGD PMID:27685844 RGD:14928335 NCBI chr  X:19,146,294...19,146,388
Ensembl chr  X:19,146,294...19,146,388
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 chr18:73,634,790...73,703,791
Ensembl chr18:73,639,009...73,703,780
JBrowse link
Klatskin's tumor term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apc APC, WNT signaling pathway regulator ISO ClinVar Annotator: match by term: Klatskin tumor ClinVar PMID:25741868 NCBI chr18:34,220,297...34,322,190
Ensembl chr18:34,220,924...34,322,552
JBrowse link
liver benign neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Aldob aldolase B, fructose-bisphosphate ISO protein:increased activity:liver (rat) RGD PMID:8264573 RGD:2313432 NCBI chr 4:49,535,993...49,549,546
Ensembl chr 4:49,535,995...49,549,546
JBrowse link
G Apobec1 apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 ISO RGD PMID:9633945 RGD:10755510 NCBI chr 6:122,577,792...122,603,024
Ensembl chr 6:122,577,792...122,602,444
JBrowse link
G Cbx7 chromobox 7 IMP RGD PMID:22214847 RGD:9587356 NCBI chr15:79,915,804...79,971,143
Ensembl chr15:79,915,807...79,971,119
JBrowse link
G Cdkn1a cyclin-dependent kinase inhibitor 1A (P21) ISO protein:increased expression:liver RGD PMID:23890812 RGD:13792775 NCBI chr17:29,090,979...29,100,722
Ensembl chr17:29,090,976...29,100,727
JBrowse link
G Col1a1 collagen, type I, alpha 1 onset ISO mRNA:increased expression:liver (rat) RGD PMID:21295105 RGD:5130894 NCBI chr11:94,936,224...94,953,042
Ensembl chr11:94,936,224...94,953,042
JBrowse link
G Eif4g2 eukaryotic translation initiation factor 4, gamma 2 IDA RGD PMID:9633945 RGD:10755510 NCBI chr 7:111,067,985...111,083,030
Ensembl chr 7:111,067,750...111,083,030
JBrowse link
G H2ax H2A.X variant histone treatment ISO RGD PMID:23474136 RGD:8693737 NCBI chr 9:44,334,715...44,336,077
Ensembl chr 9:44,334,694...44,336,077
JBrowse link
G Hspa4 heat shock protein 4 ISO protein:increased expression:liver (rat) RGD PMID:22213170 RGD:5686872 NCBI chr11:53,259,814...53,300,479
Ensembl chr11:53,259,814...53,300,457
JBrowse link
G Il10 interleukin 10 treatment ISO RGD PMID:25168696 RGD:11049493 NCBI chr 1:131,019,845...131,024,970
Ensembl chr 1:131,019,845...131,024,974
JBrowse link
G Kmt5c lysine methyltransferase 5C disease_progression ISO protein:decreased expression:liver RGD PMID:16497704 RGD:9586726 NCBI chr 7:4,740,092...4,747,514
Ensembl chr 7:4,740,115...4,747,514
JBrowse link
G Map2k3 mitogen-activated protein kinase kinase 3 ISO RGD PMID:24233520 RGD:7495808 NCBI chr11:60,932,054...60,952,811
Ensembl chr11:60,932,033...60,952,811
JBrowse link
G Met met proto-oncogene onset ISO mRNA, protein:increased expression:neoplastic liver (rat) RGD PMID:11956651 RGD:2317546 NCBI chr 6:17,463,349...17,573,980
Ensembl chr 6:17,463,800...17,573,980
JBrowse link
G Mthfr methylenetetrahydrofolate reductase onset ISO mRNA:decreased expression:liver (rat) RGD PMID:22213190 RGD:6893663 NCBI chr 4:148,039,077...148,059,562
Ensembl chr 4:148,039,077...148,059,551
JBrowse link
G Nqo1 NAD(P)H dehydrogenase, quinone 1 ISO RGD PMID:24418717 RGD:11035219 NCBI chr 8:107,388,225...107,403,205
Ensembl chr 8:107,388,225...107,403,206
JBrowse link
G Ttpa tocopherol (alpha) transfer protein ISO mRNA:decreased expression:liver RGD PMID:9178827 RGD:1600436 NCBI chr 4:20,007,894...20,030,822
Ensembl chr 4:20,007,938...20,030,785
JBrowse link
G Tut4 terminal uridylyl transferase 4 ISO human cells in a mouse model RGD PMID:24056962 RGD:11530012 NCBI chr 4:108,459,410...108,559,415
Ensembl chr 4:108,459,426...108,559,421
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 13427
    disease of anatomical entity 12903
      gastrointestinal system disease 4329
        hepatobiliary disease 2498
          hepatobiliary benign neoplasm 120
            biliary tract benign neoplasm + 93
            liver benign neoplasm + 33
Path 2
Term Annotations click to browse term
  disease 13427
    disease of anatomical entity 12903
      gastrointestinal system disease 4329
        Digestive System Neoplasms 1880
          Gastrointestinal Neoplasms 1739
            gastrointestinal system benign neoplasm 150
              hepatobiliary benign neoplasm 120
                biliary tract benign neoplasm + 93
                liver benign neoplasm + 33
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.