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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 B-Raf proto-oncogene, serine/threonine kinase ISO DNA:missense mutation:cds:p.V600E (human) RGD PMID:25704541 RGD:11521169 NCBI chr18:8,957,963...9,132,558
Ensembl chr18:8,957,959...9,132,553
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 chr 3:117,250,096...117,316,200
Ensembl chr 3:117,250,096...117,316,200
JBrowse link
G APOE apolipoprotein E susceptibility ISO DNA:SNP:intron:rs440446 (human) RGD PMID:18296645 RGD:2317550 NCBI chr 6:51,373,113...51,375,333
Ensembl chr 6:51,372,259...51,377,794
JBrowse link
G TJP1 tight junction protein 1 ISO protein:decreased expression:bile duct RGD PMID:19184677 RGD:2325030 NCBI chr 1:144,930,387...145,195,857
Ensembl chr 1:144,930,368...145,195,836
JBrowse link
bile duct carcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC100524016 mesothelin ISO protein:increased expression:bile duct RGD PMID:17276942 RGD:2326059 NCBI chr 3:41,025,892...41,029,302 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 4:71,902,891...72,107,047
Ensembl chr 4:71,903,359...72,107,046
JBrowse link
G EGFR epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chr 9:139,302,410...139,474,632
Ensembl chr 9:139,300,022...139,478,882
JBrowse link
G FSCN1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile duct RGD PMID:17419223 RGD:2317786 NCBI chr 3:4,134,173...4,143,275
Ensembl chr 3:4,134,170...4,145,394
JBrowse link
G IL6 interleukin 6 disease_progression ISO protein:increased expression:serum RGD PMID:17617204 RGD:2317166 NCBI chr 9:91,506,421...91,510,830
Ensembl chr 9:91,506,340...91,511,263
JBrowse link
G MET MET proto-oncogene, receptor tyrosine kinase ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15892172 RGD:2317585 NCBI chr18:29,426,044...29,541,526
Ensembl chr18:29,426,044...29,541,512
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 chr14:138,502,005...138,771,543
Ensembl chr14:138,499,161...138,779,938
JBrowse link
G MKI67 marker of proliferation Ki-67 disease_progression ISO RGD PMID:9869516 RGD:2317706 NCBI chr14:137,266,622...137,296,312 JBrowse link
G MUC4 mucin 4, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:16857800 RGD:2324929 NCBI chr13:134,192,412...134,248,435 JBrowse link
G NCAM1 neural cell adhesion molecule 1 disease_progression ISO RGD PMID:8501910, PMID:9851639 RGD:2326076, RGD:2326077 NCBI chr 9:40,628,602...40,960,605
Ensembl chr 9:40,628,750...40,960,608
JBrowse link
G RUNX3 RUNX family transcription factor 3 ISO DNA:hypermethylation:promoter RGD PMID:15471559 RGD:2324957 NCBI chr 6:82,531,203...82,595,044
Ensembl chr 6:82,531,215...82,595,026
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 8:69,643,427...69,663,152
Ensembl chr 8:69,531,487...69,718,304
JBrowse link
G CTPS1 CTP synthase 1 ISO mRNA:increased expression:biliary tract neoplasm (human) RGD PMID:12819026 RGD:2317903 NCBI chr 6:170,201,749...170,233,105
Ensembl chr 6:170,201,748...170,233,054
JBrowse link
G ELF3 E74 like ETS transcription factor 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr10:24,237,852...24,242,266
Ensembl chr10:24,237,068...24,243,058
JBrowse link
G FASLG 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:2317742, RGD:2317743 NCBI chr 9:115,068,314...115,075,147
Ensembl chr 9:115,068,090...115,076,475
JBrowse link
G HGF hepatocyte growth factor ISO mRNA:increased expression: : RGD PMID:12819026 RGD:2317903 NCBI chr 9:98,437,771...98,513,573
Ensembl chr 9:98,437,087...98,513,156
JBrowse link
G IL4 interleukin 4 ISO RGD PMID:18798553 RGD:2317263 NCBI chr 2:134,986,817...134,994,365
Ensembl chr 2:134,986,817...134,994,365
JBrowse link
G IL6 interleukin 6 ISO RGD PMID:18159174 RGD:2317165 NCBI chr 9:91,506,421...91,510,830
Ensembl chr 9:91,506,340...91,511,263
JBrowse link
G MDM2 MDM2 proto-oncogene ISO protein:increased expression:biliary epithelium (human) RGD PMID:16505435 RGD:2317415 NCBI chr 5:33,105,717...33,137,602
Ensembl chr 5:33,086,994...33,178,089
JBrowse link
G MTAP methylthioadenosine phosphorylase ISO RGD PMID:16373701 RGD:2317953 NCBI chr 1:200,882,954...200,934,389
Ensembl chr 1:200,882,955...200,934,639
JBrowse link
G MUC1 mucin 1, cell surface associated ISO RGD PMID:19129927 RGD:2317987 NCBI chr 4:94,626,317...94,631,194 JBrowse link
G MUC4 mucin 4, cell surface associated ISO protein:increased expression:bile,biliary tract RGD PMID:18475301 RGD:2324916 NCBI chr13:134,192,412...134,248,435 JBrowse link
G MUC5AC mucin 5AC, oligomeric mucus/gel-forming disease_progression ISO protein:increased expression:serum RGD PMID:18475301 RGD:2324916 NCBI chr 2:757,897...790,321 JBrowse link
G PRKACB protein kinase cAMP-activated catalytic subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 6:129,520,397...129,636,207
Ensembl chr 6:129,519,962...129,635,517
JBrowse link
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 chr14:110,955,698...111,038,898
Ensembl chr14:110,955,656...111,078,873
JBrowse link
G ADRB2 adrenoceptor beta 2 ISO protein:decreased expression:liver RGD PMID:16292515 RGD:2325640 NCBI chr 2:150,032,649...150,035,591
Ensembl chr 2:150,032,782...150,035,591
JBrowse link
G ALB albumin disease_progression ISO RGD PMID:10776430, PMID:17545000, PMID:20431764 RGD:2325679, RGD:2325680, RGD:2325682 NCBI chr 8:69,643,427...69,663,152
Ensembl chr 8:69,531,487...69,718,304
JBrowse link
G ALOX5 arachidonate 5-lipoxygenase ISO protein:increased expression:bile duct RGD PMID:18507031 RGD:2317521 NCBI chr14:90,859,209...90,907,084
Ensembl chr14:90,858,975...90,907,094
JBrowse link
G ANXA2 annexin A2 disease_progression ISO RGD PMID:20493868 RGD:2325728 NCBI chr 1:111,588,721...111,635,064
Ensembl chr 1:111,588,306...111,635,064
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 chr 2:116,913,354...116,985,303
Ensembl chr 2:116,812,582...117,034,912
JBrowse link
G APOA1 apolipoprotein A1 ISO protein:decreased expression:serum RGD PMID:19486127 RGD:2325756 NCBI chr 9:44,216,481...44,218,360
Ensembl chr 9:44,216,393...44,218,978
JBrowse link
G ARID1A AT-rich interaction domain 1A ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr 6:84,049,729...84,124,302
Ensembl chr 6:84,049,365...84,123,384
JBrowse link
G ASPH aspartate beta-hydroxylase ISO RGD PMID:21898484 RGD:6902945 NCBI chr 4:71,902,891...72,107,047
Ensembl chr 4:71,903,359...72,107,046
JBrowse link
G BAP1 BRCA1 associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509, PMID:25231345 NCBI chr13:34,544,570...34,553,538
Ensembl chr13:34,544,575...34,553,621
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 chr18:8,957,963...9,132,558
Ensembl chr18:8,957,959...9,132,553
JBrowse link
G CYCS cytochrome c, somatic ISO RGD PMID:19788692 RGD:2317615 NCBI chr18:47,169,921...47,172,212
Ensembl chr18:47,169,866...47,173,866
JBrowse link
G EGFR epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chr 9:139,302,410...139,474,632
Ensembl chr 9:139,300,022...139,478,882
JBrowse link
G EPO erythropoietin ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chr 3:8,620,508...8,622,936
Ensembl chr 3:8,620,508...8,622,936
JBrowse link
G EPOR erythropoietin receptor ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chr 2:70,063,601...70,068,821
Ensembl chr 2:70,063,515...70,068,821
JBrowse link
G ERBB2 erb-b2 receptor tyrosine kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635 NCBI chr12:22,591,621...22,621,384
Ensembl chr12:22,590,725...22,621,351
JBrowse link
G FASLG Fas ligand (TNF superfamily, member 6) ISO RGD PMID:11029528 RGD:2317746 NCBI chr 9:115,068,314...115,075,147
Ensembl chr 9:115,068,090...115,076,475
JBrowse link
G FGF2 fibroblast growth factor 2 ISO protein:increased expression:bile RGD PMID:11478488 RGD:2317765 NCBI chr 8:101,278,877...101,344,084
Ensembl chr 8:101,278,878...101,343,916
JBrowse link
G FGFR2 fibroblast growth factor receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr14:131,183,095...131,285,001
Ensembl chr14:131,181,710...131,579,703
JBrowse link
G FSCN1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile ducts RGD PMID:19721413 RGD:2317780 NCBI chr 3:4,134,173...4,143,275
Ensembl chr 3:4,134,170...4,145,394
JBrowse link
G GNAS GNAS complex locus disease_progression ISO DNA:polymorphism:393T>C (human)
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:17356712, PMID:22561520 RGD:1601377 NCBI chr17:58,985,580...59,053,022
Ensembl chr17:58,998,981...59,053,021
JBrowse link
G HDAC6 histone deacetylase 6 ISO protein:increased expression:liver: RGD PMID:23370327 RGD:9681560 NCBI chr  X:42,917,911...42,941,894
Ensembl chr  X:42,917,960...42,941,890
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 chr 9:98,437,771...98,513,573
Ensembl chr 9:98,437,087...98,513,156
JBrowse link
G IDH1 isocitrate dehydrogenase (NADP(+)) 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr15:111,341,153...111,362,330
Ensembl chr15:111,341,152...111,362,280
JBrowse link
G IDH2 isocitrate dehydrogenase (NADP(+)) 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr 7:55,654,298...55,675,571
Ensembl chr 7:55,651,606...55,681,426
JBrowse link
G IL4R interleukin 4 receptor ISO mRNA:increased expression:bile duct RGD PMID:18798553 RGD:2317263 NCBI chr 3:19,526,343...19,576,792
Ensembl chr 3:19,523,564...19,576,544
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 chr 9:91,506,421...91,510,830
Ensembl chr 9:91,506,340...91,511,263
JBrowse link
G KMT2C lysine methyltransferase 2C ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr18:4,993,213...5,279,668
Ensembl chr18:4,993,196...5,279,042
JBrowse link
G KRAS KRAS proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8968066, PMID:22561520 NCBI chr 5:48,508,774...48,546,260
Ensembl chr 5:48,508,790...48,549,346
JBrowse link
G KRT7 keratin 7 ISO RGD PMID:18393293 RGD:2317308 NCBI chr 5:17,553,192...17,570,582
Ensembl chr 5:17,555,714...17,571,141
JBrowse link
G LOC100524016 mesothelin ISO CTD Direct Evidence: marker/mechanism CTD PMID:14576474 NCBI chr 3:41,025,892...41,029,302 JBrowse link
G LOC100739163 glutathione S-transferase P-like treatment ISO DNA:hypermethylation:promoter
human cell line in a mouse model
RGD PMID:12805482, PMID:15467712 RGD:14401711, RGD:2317198 NCBI chr 2:4,978,761...4,982,233 JBrowse link
G MDM2 MDM2 proto-oncogene disease_progression ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15619210 RGD:2317417 NCBI chr 5:33,105,717...33,137,602
Ensembl chr 5:33,086,994...33,178,089
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 chr18:29,426,044...29,541,526
Ensembl chr18:29,426,044...29,541,512
JBrowse link
G MGMT O-6-methylguanine-DNA methyltransferase ISO DNA:hypermethylation:promoter (human) RGD PMID:17550320 RGD:2317632 NCBI chr14:138,502,005...138,771,543
Ensembl chr14:138,499,161...138,779,938
JBrowse link
G MIR155 microRNA mir-155 ISO miRNA:increased expression:serum RGD PMID:30653586 RGD:21081530 NCBI chr13:189,138,822...189,138,902
Ensembl chr13:189,138,822...189,138,902
JBrowse link
G MKI67 marker of proliferation Ki-67 disease_progression ISO RGD PMID:12903495 RGD:2317705 NCBI chr14:137,266,622...137,296,312 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 6:30,059,247...30,087,031
Ensembl chr 6:30,058,594...30,086,982
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 chr17:48,179,690...48,186,782
Ensembl chr17:48,175,056...48,188,264
JBrowse link
G MTHFR methylenetetrahydrofolate reductase susceptibility ISO DNA:polymorphism (human) RGD PMID:17201138 RGD:2317119 NCBI chr 6:71,863,637...71,882,118
Ensembl chr 6:71,863,636...71,881,820
JBrowse link
G MUC1 mucin 1, cell surface associated disease_progression ISO protein:increased expression:serum
protein:increased expression:bile duct:
protein:increased secretion:bile
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 chr 4:94,626,317...94,631,194 JBrowse link
G MUC2 mucin 2, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chr 2:689,363...719,542 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 chr13:134,192,412...134,248,435 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 chr 2:757,897...790,321 JBrowse link
G MUC5B mucin 5B, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chr 2:807,685...842,096 JBrowse link
G MUC6 mucin 6, oligomeric mucus/gel-forming ISO protein:increased expression: : RGD PMID:10209489 RGD:2325167 NCBI chr 2:630,075...657,967 JBrowse link
G NCAM1 neural cell adhesion molecule 1 ISO associated with hepatitis RGD PMID:12031086 RGD:2326079 NCBI chr 9:40,628,602...40,960,605
Ensembl chr 9:40,628,750...40,960,608
JBrowse link
G NOS2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism
protein:increased expression:bile duct
CTD
RGD
PMID:16094703, PMID:16818635 RGD:2325280 NCBI chr12:44,174,944...44,219,875
Ensembl chr12:44,174,944...44,327,111
JBrowse link
G NOTCH1 notch receptor 1 ISO protein:increased expression:cholangiocyte RGD PMID:15887117 RGD:2325330
G NR1H4 nuclear receptor subfamily 1 group H member 4 disease_progression ISO mRNA:decreased expression:liver (rat) RGD PMID:24255171 RGD:15090822 NCBI chr 5:83,607,222...83,732,668
Ensembl chr 5:83,604,288...83,684,604
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 chr13:66,038,669...66,045,478 JBrowse link
G P14ARF p14ARF protein onset ISO protein:decreased expression:liver RGD PMID:15619210 RGD:2317417 NCBI chr 1:200,774,496...200,799,149
Ensembl chr 1:200,774,496...200,798,854
JBrowse link
G PAWR pro-apoptotic WT1 regulator ISO mRNA,protein:decreased expression:cholangiocyte: RGD PMID:20724592 RGD:9835357 NCBI chr 5:101,693,145...101,797,842
Ensembl chr 5:101,692,143...101,797,835
JBrowse link
G PBRM1 polybromo 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr13:34,689,718...34,821,117
Ensembl chr13:34,689,721...34,820,957
JBrowse link
G PEG3 paternally expressed 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr 6:61,281,931...61,307,788
Ensembl chr 6:61,285,456...61,292,885
JBrowse link
G PRKACA protein kinase cAMP-activated catalytic subunit alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 2:65,074,876...65,095,564
Ensembl chr 2:65,074,870...65,095,553
JBrowse link
G PRKACB protein kinase cAMP-activated catalytic subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 6:129,520,397...129,636,207
Ensembl chr 6:129,519,962...129,635,517
JBrowse link
G PRSS2 serine protease 2 ISO protein:increased expression:serum RGD PMID:8621252 RGD:2324908 NCBI chr18:7,443,327...7,446,625
Ensembl chr18:7,443,327...7,446,625
JBrowse link
G PTEN phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:23376645, PMID:27022031 RGD:12802341 NCBI chr14:99,929,590...100,021,619 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 chr 9:127,850,164...127,858,866
Ensembl chr 9:127,850,013...127,858,884
JBrowse link
G RNF43 ring finger protein 43 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr12:34,631,574...34,695,021 JBrowse link
G ROBO2 roundabout guidance receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr13:177,365,712...179,040,027
Ensembl chr13:177,365,717...179,013,542
JBrowse link
G RUNX3 RUNX family transcription factor 3 ISO protein:decreased expression:bile duct RGD PMID:19827872 RGD:2324955 NCBI chr 6:82,531,203...82,595,044
Ensembl chr 6:82,531,215...82,595,026
JBrowse link
G SLC5A5 solute carrier family 5 member 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17408651 NCBI chr 2:59,869,157...59,885,086
Ensembl chr 2:59,869,154...59,885,265
JBrowse link
G SMAD4 SMAD family member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr 1:100,521,843...100,633,501
Ensembl chr 1:100,514,791...100,628,029
JBrowse link
G SOX17 SRY-box transcription factor 17 severity ISO RGD PMID:20816680 RGD:4889598 NCBI chr 4:76,854,218...76,857,143
Ensembl chr 4:76,852,230...76,857,139
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 chr 6:49,332,169...49,348,642
Ensembl chr 6:49,332,169...49,349,048
JBrowse link
G TGFBR2 transforming growth factor beta receptor 2 ISO mRNA:increased expression:bile duct RGD PMID:12632524 RGD:1299231 NCBI chr13:16,784,370...16,875,828
Ensembl chr13:16,784,491...16,878,165
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 chr 1:131,728,781...131,746,098
Ensembl chr 1:131,728,781...131,746,115
JBrowse link
G TNC tenascin C severity ISO RGD PMID:20816680 RGD:4889598 NCBI chr 1:255,533,235...255,630,381
Ensembl chr 1:255,532,449...255,630,377
JBrowse link
G TP53 tumor protein p53 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635, PMID:22561520 NCBI chr12:52,939,643...52,953,786
Ensembl chr12:52,939,643...52,953,819
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 chr 3:117,250,096...117,316,200
Ensembl chr 3:117,250,096...117,316,200
JBrowse link
G FSCN1 fascin actin-bundling protein 1 ISO mRNA, protein:increased expression: : RGD PMID:15136764 RGD:2317789 NCBI chr 3:4,134,173...4,143,275
Ensembl chr 3:4,134,170...4,145,394
JBrowse link
G LOC100524016 mesothelin ISO protein:increased expression:common bile duct, ampulla of vater RGD PMID:16416732 RGD:2326064 NCBI chr 3:41,025,892...41,029,302 JBrowse link
G MTAP methylthioadenosine phosphorylase ISO DNA, protein:deletion, decreased expression:common bile duct: RGD PMID:15662124 RGD:2317954 NCBI chr 1:200,882,954...200,934,389
Ensembl chr 1:200,882,955...200,934,639
JBrowse link
G MUC1 mucin 1, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:8766528 RGD:2324856 NCBI chr 4:94,626,317...94,631,194 JBrowse link
G MUC4 mucin 4, cell surface associated ISO protein:increased expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chr13:134,192,412...134,248,435 JBrowse link
G MUC5AC mucin 5AC, oligomeric mucus/gel-forming ISO protein:altered expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chr 2:757,897...790,321 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 OMIM NCBI chr14:40,868,819...40,888,322
Ensembl chr14:40,868,676...40,888,328
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 ISO DNA:mutations:multiple
associated with tuberous sclerosis;DNA:mutations:multiple
RGD PMID:22251200, PMID:29512829 RGD:21079730, RGD:21079732 NCBI chr 3:39,898,924...39,935,579
Ensembl chr 3:39,898,922...39,937,371
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 CTD Direct Evidence: marker/mechanism
mRNA,protein:increased expression:liver:
CTD
RGD
PMID:15509519 RGD:1358261 NCBI chr 5:62,406,928...62,483,690
Ensembl chr 5:62,438,017...62,485,537
JBrowse link
G CARM1 coactivator associated arginine methyltransferase 1 ISO mRNA,protein:increased expression:liver: RGD PMID:23912631 RGD:9586718 NCBI chr 2:69,602,121...69,644,862
Ensembl chr 2:69,602,130...69,644,862
JBrowse link
G CDKN1B cyclin dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:17620307 NCBI chr 5:59,731,224...59,735,831
Ensembl chr 5:59,731,206...59,735,831
JBrowse link
G CTNNB1 catenin beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21147764 NCBI chr13:25,163,550...25,208,314
Ensembl chr13:25,137,173...25,208,311
JBrowse link
G CYP2E1 cytochrome P450, family 2, subfamily E, polypeptide 1 treatment ISO RGD PMID:23543859 RGD:14700918 NCBI chr14:141,690,737...141,703,078
Ensembl chr14:141,690,426...141,736,818
JBrowse link
G HNF1A HNF1 homeobox A susceptibility ISO 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 chr14:40,868,819...40,888,322
Ensembl chr14:40,868,676...40,888,328
JBrowse link
G HP haptoglobin ISO RGD PMID:10569800 RGD:1626391 NCBI chr 6:14,980,382...14,985,245 JBrowse link
G HRAS HRas proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8200073 NCBI chr 2:299,662...302,539
Ensembl chr 2:299,660...302,501
JBrowse link
G KRAS KRAS proto-oncogene, GTPase induced ISO aflatoxin B1 induced:DNA:transversion,transition mutations:cds: RGD PMID:8446626 RGD:11568697 NCBI chr 5:48,508,774...48,546,260
Ensembl chr 5:48,508,790...48,549,346
JBrowse link
G MKI67 marker of proliferation Ki-67 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31939706 NCBI chr14:137,266,622...137,296,312 JBrowse link
G NR1H4 nuclear receptor subfamily 1 group H member 4 ISO RGD PMID:17183066 RGD:14696794 NCBI chr 5:83,607,222...83,732,668
Ensembl chr 5:83,604,288...83,684,604
JBrowse link
G NR1I3 nuclear receptor subfamily 1 group I member 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25656644 NCBI chr 4:89,226,314...89,231,781
Ensembl chr 4:89,226,690...89,236,450
JBrowse link
G PTEN phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:15199412, PMID:27022031 RGD:1302555 NCBI chr14:99,929,590...100,021,619 JBrowse link
G TMEM70 transmembrane protein 70 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr 4:61,958,605...61,966,041
Ensembl chr 4:61,958,602...61,966,027
JBrowse link
G UBE2E2 ubiquitin conjugating enzyme E2 E2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr13:9,998,097...10,380,564
Ensembl chr13:9,998,176...10,380,564
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 chr 2:116,913,354...116,985,303
Ensembl chr 2:116,812,582...117,034,912
JBrowse link
G ARID1A AT-rich interaction domain 1A disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chr 6:84,049,729...84,124,302
Ensembl chr 6:84,049,365...84,123,384
JBrowse link
G BECN1 beclin 1 disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chr12:20,041,914...20,054,249
Ensembl chr12:20,041,956...20,054,373
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 chr18:8,957,963...9,132,558
Ensembl chr18:8,957,959...9,132,553
JBrowse link
G FAS Fas cell surface death receptor disease_progression ISO RGD PMID:11003620 RGD:14700701 NCBI chr14:100,927,305...100,954,781 JBrowse link
G FASLG Fas ligand (TNF superfamily, member 6) severity ISO RGD PMID:11003620 RGD:14700701 NCBI chr 9:115,068,314...115,075,147
Ensembl chr 9:115,068,090...115,076,475
JBrowse link
G FOXP3 forkhead box P3 ISO DNA:hypomethylation:liver RGD PMID:24291052 RGD:38599002 NCBI chr  X:43,303,777...43,328,164
Ensembl chr  X:43,303,782...43,328,735
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 chr15:111,341,153...111,362,330
Ensembl chr15:111,341,152...111,362,280
JBrowse link
G IDH2 isocitrate dehydrogenase (NADP(+)) 2 disease_progression ISO DNA:mutations: : RGD PMID:22824796 RGD:14985256 NCBI chr 7:55,654,298...55,675,571
Ensembl chr 7:55,651,606...55,681,426
JBrowse link
G KRAS KRAS proto-oncogene, GTPase disease_progression ISO DNA:mutations:: RGD PMID:24139215 RGD:14398746 NCBI chr 5:48,508,774...48,546,260
Ensembl chr 5:48,508,790...48,549,346
JBrowse link
G MIR152 microRNA mir-152 ISO miRNA:decreased expression:intrahepatic bile duct RGD PMID:28921383 RGD:19165148 NCBI chr12:24,292,249...24,292,328
Ensembl chr12:24,292,251...24,292,336
JBrowse link
G MIR21 microRNA mir-21 ISO RNA:increased expression:liver,plasma RGD PMID:27685844 RGD:14928335 NCBI chr12:36,065,267...36,065,358
Ensembl chr12:36,065,267...36,065,358
JBrowse link
G MIR221 microRNA mir-221 severity ISO RGD PMID:27685844 RGD:14928335 NCBI chr  X:40,571,068...40,571,137
Ensembl chr  X:40,571,068...40,571,137
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 chr 1:100,521,843...100,633,501
Ensembl chr 1:100,514,791...100,628,029
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 NCBI chr 2:116,913,354...116,985,303
Ensembl chr 2:116,812,582...117,034,912
JBrowse link
liver benign neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ALDOB aldolase, fructose-bisphosphate B ISO protein:increased activity:liver (rat) RGD PMID:8264573 RGD:2313432 NCBI chr 1:243,127,870...243,141,504
Ensembl chr 1:243,110,585...243,141,418
JBrowse link
G APOBEC1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 ISO RGD PMID:9633945 RGD:10755510 NCBI chr 5:62,811,819...62,820,532
Ensembl chr 5:62,810,879...62,820,173
JBrowse link
G CBX7 chromobox 7 ISO RGD PMID:22214847 RGD:9587356 NCBI chr 5:9,070,312...9,090,467 JBrowse link
G CDKN1A cyclin dependent kinase inhibitor 1A ISO protein:increased expression:liver RGD PMID:23890812 RGD:13792775 NCBI chr 7:32,354,776...32,363,771
Ensembl chr 7:32,359,455...32,363,761
JBrowse link
G COL1A1 collagen type I alpha 1 chain onset ISO mRNA:increased expression:liver (rat) RGD PMID:21295105 RGD:5130894 NCBI chr12:26,379,087...26,397,180
Ensembl chr12:26,379,090...26,397,003
JBrowse link
G EIF4G2 eukaryotic translation initiation factor 4 gamma 2 ISO RGD PMID:9633945 RGD:10755510 NCBI chr 2:48,666,590...48,678,656
Ensembl chr 2:48,625,268...48,726,768
JBrowse link
G HSPA4 heat shock protein family A (Hsp70) member 4 ISO protein:increased expression:liver (rat) RGD PMID:22213170 RGD:5686872 NCBI chr 2:135,345,724...135,391,112
Ensembl chr 2:135,305,749...135,394,185
JBrowse link
G IL10 interleukin 10 treatment ISO RGD PMID:25168696 RGD:11049493 NCBI chr 9:67,400,727...67,405,941
Ensembl chr 9:67,400,727...67,405,711
JBrowse link
G KMT5C lysine methyltransferase 5C disease_progression ISO protein:decreased expression:liver RGD PMID:16497704 RGD:9586726 NCBI chr 6:59,517,058...59,524,551
Ensembl chr 6:59,517,058...59,525,434
JBrowse link
G LOC100522201 histone H2AX treatment ISO RGD PMID:23474136 RGD:8693737 NCBI chr 9:46,308,824...46,310,494
Ensembl chr 9:46,309,653...46,310,084
JBrowse link
G MAP2K3 mitogen-activated protein kinase kinase 3 ISO RGD PMID:24233520 RGD:7495808 NCBI chr12:61,396,337...61,417,333
Ensembl chr12:61,396,331...61,421,579
JBrowse link
G MET MET proto-oncogene, receptor tyrosine kinase onset ISO mRNA, protein:increased expression:neoplastic liver (rat) RGD PMID:11956651 RGD:2317546 NCBI chr18:29,426,044...29,541,526
Ensembl chr18:29,426,044...29,541,512
JBrowse link
G MTHFR methylenetetrahydrofolate reductase onset ISO mRNA:decreased expression:liver (rat) RGD PMID:22213190 RGD:6893663 NCBI chr 6:71,863,637...71,882,118
Ensembl chr 6:71,863,636...71,881,820
JBrowse link
G NQO1 NAD(P)H quinone dehydrogenase 1 ISO RGD PMID:24418717 RGD:11035219 NCBI chr 6:17,292,962...17,302,593
Ensembl chr 6:17,292,769...17,302,590
JBrowse link
G TTPA alpha tocopherol transfer protein ISO mRNA:decreased expression:liver RGD PMID:9178827 RGD:1600436 NCBI chr 4:70,960,580...70,980,883
Ensembl chr 4:70,961,465...71,021,839
JBrowse link
G TUT4 terminal uridylyl transferase 4 ISO human cells in a mouse model RGD PMID:24056962 RGD:11530012 NCBI chr 6:159,655,658...159,794,450
Ensembl chr 6:159,655,627...159,793,758
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 12641
    disease of anatomical entity 12177
      gastrointestinal system disease 4036
        hepatobiliary disease 2310
          hepatobiliary benign neoplasm 110
            biliary tract benign neoplasm + 84
            liver benign neoplasm + 32
Path 2
Term Annotations click to browse term
  disease 12641
    disease of anatomical entity 12177
      gastrointestinal system disease 4036
        Digestive System Neoplasms 1794
          Gastrointestinal Neoplasms 1667
            gastrointestinal system benign neoplasm 140
              hepatobiliary benign neoplasm 110
                biliary tract benign neoplasm + 84
                liver benign neoplasm + 32
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.