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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 chr16:8,222,909...8,318,179
Ensembl chr16:8,222,907...8,317,906
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 chr17:15,877,937...15,916,032
Ensembl chr17:15,878,244...15,915,135
JBrowse link
G APOE apolipoprotein E susceptibility ISO DNA:SNP:intron:rs440446 (human) RGD PMID:18296645 RGD:2317550 NCBI chr 1:110,525,717...110,528,534
Ensembl chr 1:110,525,722...110,528,440
JBrowse link
G TJP1 tight junction protein 1 ISO protein:decreased expression:bile duct RGD PMID:19184677 RGD:2325030 NCBI chr 3:38,997,122...39,076,617
Ensembl chr 3:38,997,076...39,241,574
JBrowse link
bile duct carcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC611363 mesothelin ISO protein:increased expression:bile duct RGD PMID:17276942 RGD:2326059 NCBI chr 6:39,827,985...39,834,945 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 chr29:11,812,275...12,022,755
Ensembl chr29:11,814,554...12,022,680
JBrowse link
G EGFR epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chr18:5,983,669...6,044,092
Ensembl chr18:5,982,770...6,042,631
JBrowse link
G FSCN1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile duct RGD PMID:17419223 RGD:2317786 NCBI chr 6:12,360,849...12,370,906
Ensembl chr 6:12,354,599...12,370,808
JBrowse link
G IL6 interleukin 6 disease_progression ISO protein:increased expression:serum RGD PMID:17617204 RGD:2317166 NCBI chr14:36,474,268...36,478,519
Ensembl chr14:36,473,394...36,478,519
JBrowse link
G LOC476718 mucin-16 ISO protein:increased expression:serum,bile RGD PMID:1657243 RGD:2325134 NCBI chr20:51,790,036...51,876,801 JBrowse link
G MET MET proto-oncogene, receptor tyrosine kinase ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15892172 RGD:2317585 NCBI chr14:55,599,047...55,711,626
Ensembl chr14:55,598,337...55,724,027
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 chr28:38,204,611...38,427,482
Ensembl chr28:38,204,610...38,427,380
JBrowse link
G MKI67 marker of proliferation Ki-67 disease_progression ISO RGD PMID:9869516 RGD:2317706 NCBI chr28:36,920,679...36,939,336
Ensembl chr28:36,913,023...36,939,486
JBrowse link
G MUC4 mucin 4, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:16857800 RGD:2324929 NCBI chr33:29,061,372...29,084,938
Ensembl chr33:29,063,096...29,111,802
JBrowse link
G NCAM1 neural cell adhesion molecule 1 disease_progression ISO RGD PMID:8501910, PMID:9851639 RGD:2326076, RGD:2326077 NCBI chr 5:19,895,587...20,192,334
Ensembl chr 5:19,895,613...20,191,995
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 chr13:62,133,747...62,169,349
Ensembl chr13:62,053,814...62,294,709
JBrowse link
G CTPS1 CTP synthase 1 ISO mRNA:increased expression:biliary tract neoplasm (human) RGD PMID:12819026 RGD:2317903 NCBI chr15:2,067,767...2,093,014
Ensembl chr15:2,067,763...2,093,014
JBrowse link
G ELF3 E74 like ETS transcription factor 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 7:959,408...965,533
Ensembl chr 7:859,585...963,788
JBrowse link
G FASLG Fas ligand 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 7:26,335,837...26,344,224
Ensembl chr 7:26,335,846...26,344,224
JBrowse link
G HGF hepatocyte growth factor ISO mRNA:increased expression: : RGD PMID:12819026 RGD:2317903 NCBI chr18:21,329,688...21,410,257
Ensembl chr18:21,332,817...21,410,263
JBrowse link
G IL4 interleukin 4 ISO RGD PMID:18798553 RGD:2317263 NCBI chr11:20,972,693...20,981,539
Ensembl chr11:20,972,690...20,981,534
JBrowse link
G IL6 interleukin 6 ISO RGD PMID:18159174 RGD:2317165 NCBI chr14:36,474,268...36,478,519
Ensembl chr14:36,473,394...36,478,519
JBrowse link
G MDM2 MDM2 proto-oncogene ISO protein:increased expression:biliary epithelium (human) RGD PMID:16505435 RGD:2317415 NCBI chr10:10,936,288...10,963,118
Ensembl chr10:10,893,719...10,962,596
JBrowse link
G MTAP methylthioadenosine phosphorylase ISO RGD PMID:16373701 RGD:2317953 NCBI chr11:41,148,389...41,200,635
Ensembl chr11:41,148,404...41,264,504
JBrowse link
G MUC1 mucin 1, cell surface associated ISO RGD PMID:19129927 RGD:2317987 NCBI chr 7:42,338,939...42,344,690
Ensembl chr 7:42,340,375...42,344,690
JBrowse link
G MUC4 mucin 4, cell surface associated ISO protein:increased expression:bile,biliary tract RGD PMID:18475301 RGD:2324916 NCBI chr33:29,061,372...29,084,938
Ensembl chr33:29,063,096...29,111,802
JBrowse link
G MUC5AC mucin 5AC, oligomeric mucus/gel-forming disease_progression ISO protein:increased expression:serum RGD PMID:18475301 RGD:2324916 NCBI chr18:45,471,232...45,498,961 JBrowse link
G PRKACB protein kinase cAMP-activated catalytic subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 6:63,615,445...63,729,386
Ensembl chr 6:63,618,323...63,730,146
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 chr28:12,670,885...12,740,124
Ensembl chr28:12,670,885...12,740,740
JBrowse link
G ADRB2 adrenoceptor beta 2 ISO protein:decreased expression:liver RGD PMID:16292515 RGD:2325640 NCBI chr 4:60,048,502...60,050,447
Ensembl chr 4:59,941,517...60,050,298
JBrowse link
G ALB albumin disease_progression ISO RGD PMID:10776430, PMID:17545000, PMID:20431764 RGD:2325679, RGD:2325680, RGD:2325682 NCBI chr13:62,133,747...62,169,349
Ensembl chr13:62,053,814...62,294,709
JBrowse link
G ALOX5 arachidonate 5-lipoxygenase ISO protein:increased expression:bile duct RGD PMID:18507031 RGD:2317521 NCBI chr28:2,170,920...2,218,765
Ensembl chr28:2,170,920...2,219,609
JBrowse link
G ANXA2 annexin A2 disease_progression ISO RGD PMID:20493868 RGD:2325728 NCBI chr30:25,176,845...25,210,244
Ensembl chr30:25,115,842...25,218,281
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 3:252,052...380,506
Ensembl chr 3:253,081...322,993
JBrowse link
G APOA1 apolipoprotein A1 ISO protein:decreased expression:serum RGD PMID:19486127 RGD:2325756 NCBI chr 5:16,740,071...16,742,081
Ensembl chr 5:16,740,130...16,741,943
JBrowse link
G ARID1A AT-rich interaction domain 1A ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr 2:73,331,606...73,401,151
Ensembl chr 2:73,324,852...73,401,102
JBrowse link
G ASPH aspartate beta-hydroxylase ISO RGD PMID:21898484 RGD:6902945 NCBI chr29:11,812,275...12,022,755
Ensembl chr29:11,814,554...12,022,680
JBrowse link
G B9D2 B9 domain containing 2 disease_progression ISO protein:increased expression:pancreas RGD PMID:12632524, PMID:16083599 RGD:1299231, RGD:2325020 NCBI chr 1:112,621,832...112,627,726
Ensembl chr 1:112,621,633...112,643,885
JBrowse link
G BAP1 BRCA1 associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509, PMID:25231345 NCBI chr20:37,355,499...37,364,298
Ensembl chr20:37,355,494...37,511,125
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 chr16:8,222,909...8,318,179
Ensembl chr16:8,222,907...8,317,906
JBrowse link
G CYCS cytochrome c, somatic ISO RGD PMID:19788692 RGD:2317615 NCBI chr14:38,579,446...38,581,983
Ensembl chr14:38,579,446...38,581,983
JBrowse link
G EGFR epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chr18:5,983,669...6,044,092
Ensembl chr18:5,982,770...6,042,631
JBrowse link
G EPO erythropoietin ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chr 6:8,994,211...8,995,954
Ensembl chr 6:8,994,211...8,996,144
JBrowse link
G EPOR erythropoietin receptor ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chr20:49,945,777...49,950,856
Ensembl chr20:49,945,777...49,950,856
JBrowse link
G ERBB2 erb-b2 receptor tyrosine kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635 NCBI chr 9:22,760,373...22,785,367
Ensembl chr 9:22,759,256...22,785,294
JBrowse link
G FASLG Fas ligand ISO RGD PMID:11029528 RGD:2317746 NCBI chr 7:26,335,837...26,344,224
Ensembl chr 7:26,335,846...26,344,224
JBrowse link
G FGF2 fibroblast growth factor 2 ISO protein:increased expression:bile RGD PMID:11478488 RGD:2317765 NCBI chr19:17,403,288...17,463,143
Ensembl chr19:16,994,661...17,463,151
JBrowse link
G FGFR2 fibroblast growth factor receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr28:31,303,882...31,411,015
Ensembl chr28:31,303,894...31,411,621
JBrowse link
G FSCN1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile ducts RGD PMID:19721413 RGD:2317780 NCBI chr 6:12,360,849...12,370,906
Ensembl chr 6:12,354,599...12,370,808
JBrowse link
G GNAS GNAS complex locus disease_progression ISO CTD Direct Evidence: marker/mechanism
DNA:polymorphism:393T>C (human)
CTD
RGD
PMID:17356712, PMID:22561520 RGD:1601377 NCBI chr24:43,643,409...43,658,641
Ensembl chr24:43,643,405...43,658,657
JBrowse link
G GSTP1 glutathione S-transferase pi 1 treatment ISO DNA:hypermethylation:promoter
human cell line in a mouse model
RGD PMID:12805482, PMID:15467712 RGD:14401711, RGD:2317198 NCBI chr18:49,905,161...49,908,182
Ensembl chr18:49,905,161...49,908,182
JBrowse link
G HDAC6 histone deacetylase 6 ISO protein:increased expression:liver: RGD PMID:23370327 RGD:9681560 NCBI chr  X:42,004,268...42,024,726
Ensembl chr  X:42,004,591...42,024,427
JBrowse link
G HGF hepatocyte growth factor ISO protein:increased expression:serum
mRNA, protein:increased expression: :
RGD PMID:10827151, PMID:16974053 RGD:2317909, RGD:2317925 NCBI chr18:21,329,688...21,410,257
Ensembl chr18:21,332,817...21,410,263
JBrowse link
G IDH1 isocitrate dehydrogenase (NADP(+)) 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr37:16,512,027...16,531,269
Ensembl chr37:16,512,770...16,531,219
JBrowse link
G IDH2 isocitrate dehydrogenase (NADP(+)) 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr 3:53,070,462...53,077,566
Ensembl chr 3:53,070,695...53,087,496
JBrowse link
G IL4R interleukin 4 receptor ISO mRNA:increased expression:bile duct RGD PMID:18798553 RGD:2317263 NCBI chr 6:19,254,183...19,280,973
Ensembl chr 6:19,254,487...19,389,291
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 chr14:36,474,268...36,478,519
Ensembl chr14:36,473,394...36,478,519
JBrowse link
G KMT2C lysine methyltransferase 2C ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr16:15,962,045...16,117,601
Ensembl chr16:15,963,901...16,158,408
JBrowse link
G KRAS KRAS proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8968066, PMID:22561520 NCBI chr27:22,261,753...22,296,704
Ensembl chr27:22,257,941...22,293,369
JBrowse link
G KRT7 keratin 7 ISO RGD PMID:18393293 RGD:2317308 NCBI chr27:2,812,709...2,827,451 JBrowse link
G LOC476718 mucin-16 ISO associated with Opisthorchiasis;protein:increased expression:serum RGD PMID:1653472 RGD:2325142 NCBI chr20:51,790,036...51,876,801 JBrowse link
G LOC611363 mesothelin ISO CTD Direct Evidence: marker/mechanism CTD PMID:14576474 NCBI chr 6:39,827,985...39,834,945 JBrowse link
G MDM2 MDM2 proto-oncogene disease_progression ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15619210 RGD:2317417 NCBI chr10:10,936,288...10,963,118
Ensembl chr10:10,893,719...10,962,596
JBrowse link
G MET MET proto-oncogene, receptor tyrosine kinase disease_progression ISO protein:increased expression:liver, biliary epithelium (rat)
protein:increased phosphorylation:liver, carcinoma (human)
RGD PMID:14656942, PMID:16818635 RGD:2317578, RGD:2317601 NCBI chr14:55,599,047...55,711,626
Ensembl chr14:55,598,337...55,724,027
JBrowse link
G MGMT O-6-methylguanine-DNA methyltransferase ISO DNA:hypermethylation:promoter (human) RGD PMID:17550320 RGD:2317632 NCBI chr28:38,204,611...38,427,482
Ensembl chr28:38,204,610...38,427,380
JBrowse link
G MIR155 microRNA mir-155 ISO miRNA:increased expression:serum RGD PMID:30653586 RGD:21081530 NCBI chr31:21,078,768...21,078,828
Ensembl chr31:21,078,758...21,078,833
JBrowse link
G MKI67 marker of proliferation Ki-67 disease_progression ISO RGD PMID:12903495 RGD:2317705 NCBI chr28:36,920,679...36,939,336
Ensembl chr28:36,913,023...36,939,486
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 2:60,471,092...60,492,991
Ensembl chr 2:60,471,257...60,494,113
JBrowse link
G MMP9 matrix metallopeptidase 9 ISO mRNA:increased expression:bile duct
protein:increased expression:bile duct
RGD PMID:15213623, PMID:16463672 RGD:2324667, RGD:2325856 NCBI chr24:33,274,260...33,281,116
Ensembl chr24:33,274,268...33,281,293
JBrowse link
G MTHFR methylenetetrahydrofolate reductase susceptibility ISO DNA:polymorphism (human) RGD PMID:17201138 RGD:2317119 NCBI chr 2:84,445,526...84,457,435
Ensembl chr 2:84,380,919...84,536,818
JBrowse link
G MUC1 mucin 1, cell surface associated disease_progression ISO protein:increased expression:serum
protein:increased secretion:bile
mRNA:increased expression:bile duct
protein: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 7:42,338,939...42,344,690
Ensembl chr 7:42,340,375...42,344,690
JBrowse link
G MUC2 mucin 2, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chr18:45,416,347...45,438,226 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 chr33:29,061,372...29,084,938
Ensembl chr33:29,063,096...29,111,802
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 chr18:45,471,232...45,498,961 JBrowse link
G MUC5B mucin 5B, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chr18:45,517,479...45,545,765
Ensembl chr18:45,517,474...45,545,184
JBrowse link
G MUC6 mucin 6, oligomeric mucus/gel-forming ISO protein:increased expression: : RGD PMID:10209489 RGD:2325167 NCBI chr18:45,359,412...45,376,678 JBrowse link
G NCAM1 neural cell adhesion molecule 1 ISO associated with hepatitis RGD PMID:12031086 RGD:2326079 NCBI chr 5:19,895,587...20,192,334
Ensembl chr 5:19,895,613...20,191,995
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 chr 9:42,171,821...42,210,217
Ensembl chr 9:42,171,821...42,208,588
JBrowse link
G NOTCH1 notch receptor 1 ISO protein:increased expression:cholangiocyte RGD PMID:15887117 RGD:2325330 NCBI chr 9:48,975,972...49,018,985
Ensembl chr 9:48,974,757...49,017,277
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 chr15:39,497,313...39,608,120
Ensembl chr15:39,536,290...39,608,116
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 chr20:8,486,150...8,491,448
Ensembl chr20:8,480,005...8,491,264
JBrowse link
G PAWR pro-apoptotic WT1 regulator ISO mRNA,protein:decreased expression:cholangiocyte: RGD PMID:20724592 RGD:9835357 NCBI chr15:22,114,014...22,159,287 JBrowse link
G PBRM1 polybromo 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chr20:37,110,437...37,231,676
Ensembl chr20:37,110,766...37,229,203
JBrowse link
G PEG3 paternally expressed 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr 1:101,091,161...101,123,552
Ensembl chr 1:101,098,669...101,121,032
JBrowse link
G PRKACA protein kinase cAMP-activated catalytic subunit alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr20:48,416,730...48,425,237
Ensembl chr20:48,409,045...48,426,669
JBrowse link
G PRKACB protein kinase cAMP-activated catalytic subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chr 6:63,615,445...63,729,386
Ensembl chr 6:63,618,323...63,730,146
JBrowse link
G PTEN phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:23376645, PMID:27022031 RGD:12802341 NCBI chr26:37,853,148...37,913,176
Ensembl chr26:37,835,661...37,913,176
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 7:19,668,079...19,674,903
Ensembl chr 7:19,668,082...19,674,903
JBrowse link
G RNF43 ring finger protein 43 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr 9:32,996,668...33,061,781
Ensembl chr 9:32,997,937...33,060,313
JBrowse link
G ROBO2 roundabout guidance receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr31:9,415,390...11,047,710
Ensembl chr31:9,419,026...11,022,392
JBrowse link
G SLC5A5 solute carrier family 5 member 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17408651 NCBI chr20:45,017,939...45,030,598
Ensembl chr20:45,018,119...45,030,209
JBrowse link
G SMAD4 SMAD family member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chr 1:23,875,989...23,930,027
Ensembl chr 1:23,882,139...23,969,405
JBrowse link
G SOX17 SRY-box transcription factor 17 severity ISO RGD PMID:20816680 RGD:4889598 NCBI chr29:5,979,092...5,981,504
Ensembl chr29:5,979,261...5,981,124
JBrowse link
G TGFBR2 transforming growth factor beta receptor 2 ISO mRNA:increased expression:bile duct RGD PMID:12632524 RGD:1299231 NCBI chr23:13,886,869...13,946,480
Ensembl chr23:13,889,000...13,977,636
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 chr30:6,770,212...6,786,875
Ensembl chr30:6,769,470...6,784,915
JBrowse link
G TNC tenascin C severity ISO RGD PMID:20816680 RGD:4889598 NCBI chr11:69,077,532...69,169,673
Ensembl chr11:69,077,535...69,170,281
JBrowse link
G TP53 tumor protein p53 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635, PMID:22561520 NCBI chr 5:32,561,406...32,565,149
Ensembl chr 5:32,560,598...32,574,109
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 chr17:15,877,937...15,916,032
Ensembl chr17:15,878,244...15,915,135
JBrowse link
G FSCN1 fascin actin-bundling protein 1 ISO mRNA, protein:increased expression: : RGD PMID:15136764 RGD:2317789 NCBI chr 6:12,360,849...12,370,906
Ensembl chr 6:12,354,599...12,370,808
JBrowse link
G LOC611363 mesothelin ISO protein:increased expression:common bile duct, ampulla of vater RGD PMID:16416732 RGD:2326064 NCBI chr 6:39,827,985...39,834,945 JBrowse link
G MTAP methylthioadenosine phosphorylase ISO DNA, protein:deletion, decreased expression:common bile duct: RGD PMID:15662124 RGD:2317954 NCBI chr11:41,148,389...41,200,635
Ensembl chr11:41,148,404...41,264,504
JBrowse link
G MUC1 mucin 1, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:8766528 RGD:2324856 NCBI chr 7:42,338,939...42,344,690
Ensembl chr 7:42,340,375...42,344,690
JBrowse link
G MUC4 mucin 4, cell surface associated ISO protein:increased expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chr33:29,061,372...29,084,938
Ensembl chr33:29,063,096...29,111,802
JBrowse link
G MUC5AC mucin 5AC, oligomeric mucus/gel-forming ISO protein:altered expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chr18:45,471,232...45,498,961 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 chr26:16,805,690...16,826,065
Ensembl chr26:16,805,690...16,824,790
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 6:38,865,509...38,898,977
Ensembl chr 6:38,865,507...38,898,960
JBrowse link
hepatocellular adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CARM1 coactivator associated arginine methyltransferase 1 ISO mRNA,protein:increased expression:liver: RGD PMID:23912631 RGD:9586718 NCBI chr20:50,328,466...50,371,845
Ensembl chr20:50,331,030...50,348,195
JBrowse link
G CDKN1B cyclin dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:17620307 NCBI chr27:33,609,154...33,613,558
Ensembl chr27:33,611,760...33,612,906
JBrowse link
G CTNNB1 catenin beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21147764 NCBI chr23:10,559,722...10,572,933
Ensembl chr23:10,559,718...10,572,927
JBrowse link
G CYP2E1 cytochrome P450 family 2 subfamily E member 1 treatment ISO RGD PMID:23543859 RGD:14700918 NCBI chr28:41,079,164...41,089,188
Ensembl chr28:41,035,025...41,122,754
JBrowse link
G HNF1A HNF1 homeobox A susceptibility ISO DNA:frameshift mutation, non-sense mutation:cds:R229X, G55fsX57 (human)
DNA:loss of heterozygosity, mutations:multiple
RGD PMID:12355088, PMID:14598263 RGD:14700683, RGD:14700774 NCBI chr26:16,805,690...16,826,065
Ensembl chr26:16,805,690...16,824,790
JBrowse link
G HRAS HRas proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8200073 NCBI chr18:25,642,844...25,644,717
Ensembl chr18:25,642,844...25,644,717
JBrowse link
G KRAS KRAS proto-oncogene, GTPase induced ISO aflatoxin B1 induced:DNA:transversion,transition mutations:cds: RGD PMID:8446626 RGD:11568697 NCBI chr27:22,261,753...22,296,704
Ensembl chr27:22,257,941...22,293,369
JBrowse link
G LOC477699 alpha-2-macroglobulin ISO mRNA,protein:increased expression:liver:
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:15509519 RGD:1358261 NCBI chr27:36,654,328...36,695,775 JBrowse link
G LOC479668 haptoglobin-like ISO RGD PMID:10569800 RGD:1626391 NCBI chr 5:77,795,183...77,800,034 JBrowse link
G MKI67 marker of proliferation Ki-67 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31939706 NCBI chr28:36,920,679...36,939,336
Ensembl chr28:36,913,023...36,939,486
JBrowse link
G NR1H4 nuclear receptor subfamily 1 group H member 4 ISO RGD PMID:17183066 RGD:14696794 NCBI chr15:39,497,313...39,608,120
Ensembl chr15:39,536,290...39,608,116
JBrowse link
G NR1I3 nuclear receptor subfamily 1 group I member 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25656644 NCBI chr38:21,252,874...21,257,951
Ensembl chr38:21,253,089...21,258,827
JBrowse link
G PTEN phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:15199412, PMID:27022031 RGD:1302555 NCBI chr26:37,853,148...37,913,176
Ensembl chr26:37,835,661...37,913,176
JBrowse link
G TMEM70 transmembrane protein 70 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr29:22,475,961...22,487,920
Ensembl chr29:22,478,941...22,487,741
JBrowse link
G UBE2E2 ubiquitin conjugating enzyme E2 E2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr23:20,110,128...20,593,767
Ensembl chr23:20,130,230...20,486,399
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 3:252,052...380,506
Ensembl chr 3:253,081...322,993
JBrowse link
G ARID1A AT-rich interaction domain 1A disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chr 2:73,331,606...73,401,151
Ensembl chr 2:73,324,852...73,401,102
JBrowse link
G BECN1 beclin 1 disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chr 9:20,204,203...20,215,081
Ensembl chr 9:20,204,220...20,214,236
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 chr16:8,222,909...8,318,179
Ensembl chr16:8,222,907...8,317,906
JBrowse link
G FAS Fas cell surface death receptor disease_progression ISO RGD PMID:11003620 RGD:14700701 NCBI chr26:38,738,811...38,763,298
Ensembl chr26:38,737,611...38,763,321
JBrowse link
G FASLG Fas ligand severity ISO RGD PMID:11003620 RGD:14700701 NCBI chr 7:26,335,837...26,344,224
Ensembl chr 7:26,335,846...26,344,224
JBrowse link
G FOXP3 forkhead box P3 ISO DNA:hypomethylation:liver RGD PMID:24291052 RGD:38599002 NCBI chr  X:42,331,229...42,362,841
Ensembl chr  X:42,344,108...42,350,758
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 chr37:16,512,027...16,531,269
Ensembl chr37:16,512,770...16,531,219
JBrowse link
G IDH2 isocitrate dehydrogenase (NADP(+)) 2 disease_progression ISO DNA:mutations: : RGD PMID:22824796 RGD:14985256 NCBI chr 3:53,070,462...53,077,566
Ensembl chr 3:53,070,695...53,087,496
JBrowse link
G KRAS KRAS proto-oncogene, GTPase disease_progression ISO DNA:mutations:: RGD PMID:24139215 RGD:14398746 NCBI chr27:22,261,753...22,296,704
Ensembl chr27:22,257,941...22,293,369
JBrowse link
G MIR152 microRNA mir-152 ISO miRNA:decreased expression:intrahepatic bile duct RGD PMID:28921383 RGD:19165148 NCBI chr 9:24,335,161...24,335,219
Ensembl chr 9:24,335,146...24,335,225
JBrowse link
G MIR200B microRNA mir-200b ISO RNA:increased expression:liver RGD PMID:27685844 RGD:14928335 NCBI chr 5:56,368,400...56,368,479
Ensembl chr 5:56,368,400...56,368,479
JBrowse link
G MIR21 microRNA mir-21 ISO RNA:increased expression:liver,plasma RGD PMID:27685844 RGD:14928335 NCBI chr 9:34,340,550...34,340,609
Ensembl chr 9:34,340,533...34,340,624
JBrowse link
G MIR221 microRNA mir-221 severity ISO RGD PMID:27685844 RGD:14928335 NCBI chr  X:39,523,890...39,523,951
Ensembl chr  X:39,523,885...39,523,954
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 1:23,875,989...23,930,027
Ensembl chr 1:23,882,139...23,969,405
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 3:252,052...380,506
Ensembl chr 3:253,081...322,993
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 chr11:58,150,621...58,166,266
Ensembl chr11:58,150,967...58,176,319
JBrowse link
G APOBEC1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 ISO RGD PMID:9633945 RGD:10755510 NCBI chr27:37,102,728...37,114,084
Ensembl chr27:37,103,016...37,114,556
JBrowse link
G CBX7 chromobox 7 ISO RGD PMID:22214847 RGD:9587356 NCBI chr10:25,876,022...25,896,284
Ensembl chr10:25,876,016...25,893,501
JBrowse link
G CDKN1A cyclin dependent kinase inhibitor 1A ISO protein:increased expression:liver RGD PMID:23890812 RGD:13792775 NCBI chr12:5,746,898...5,755,103
Ensembl chr12:5,745,852...5,892,281
JBrowse link
G COL1A1 collagen type I alpha 1 chain onset ISO mRNA:increased expression:liver (rat) RGD PMID:21295105 RGD:5130894 NCBI chr 9:26,183,852...26,199,927
Ensembl chr 9:26,183,852...26,199,927
JBrowse link
G EIF4G2 eukaryotic translation initiation factor 4 gamma 2 ISO RGD PMID:9633945 RGD:10755510 NCBI chr21:33,967,908...33,980,017
Ensembl chr21:33,952,793...33,977,653
JBrowse link
G H2AX H2A.X variant histone treatment ISO RGD PMID:23474136 RGD:8693737 NCBI chr 5:14,765,625...14,766,590
Ensembl chr 5:14,766,126...14,766,557
JBrowse link
G HSPA4 heat shock protein family A (Hsp70) member 4 ISO protein:increased expression:liver (rat) RGD PMID:22213170 RGD:5686872 NCBI chr11:21,290,603...21,363,701
Ensembl chr11:21,290,621...21,505,122
JBrowse link
G IL10 interleukin 10 treatment ISO RGD PMID:25168696 RGD:11049493 NCBI chr 7:5,933,285...5,937,057
Ensembl chr 7:5,933,285...5,937,057
JBrowse link
G KMT5C lysine methyltransferase 5C disease_progression ISO protein:decreased expression:liver RGD PMID:16497704 RGD:9586726 NCBI chr 1:102,334,687...102,342,090
Ensembl chr 1:102,333,543...102,342,118
JBrowse link
G MAP2K3 mitogen-activated protein kinase kinase 3 ISO RGD PMID:24233520 RGD:7495808 NCBI chr 5:42,732,751...42,762,420
Ensembl chr 5:42,700,836...42,761,736
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 chr14:55,599,047...55,711,626
Ensembl chr14:55,598,337...55,724,027
JBrowse link
G MTHFR methylenetetrahydrofolate reductase onset ISO mRNA:decreased expression:liver (rat) RGD PMID:22213190 RGD:6893663 NCBI chr 2:84,445,526...84,457,435
Ensembl chr 2:84,380,919...84,536,818
JBrowse link
G NQO1 NAD(P)H quinone dehydrogenase 1 ISO RGD PMID:24418717 RGD:11035219 NCBI chr 5:79,979,593...79,990,875
Ensembl chr 5:79,978,865...79,989,860
JBrowse link
G TTPA alpha tocopherol transfer protein ISO mRNA:decreased expression:liver RGD PMID:9178827 RGD:1600436 NCBI chr29:13,177,690...13,198,910
Ensembl chr29:13,182,308...13,192,553
JBrowse link
G TUT4 terminal uridylyl transferase 4 ISO human cells in a mouse model RGD PMID:24056962 RGD:11530012 NCBI chr15:8,832,208...8,958,136
Ensembl chr15:8,832,199...9,047,152
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 12699
    disease of anatomical entity 12239
      gastrointestinal system disease 4073
        hepatobiliary disease 2325
          hepatobiliary benign neoplasm 109
            biliary tract benign neoplasm + 83
            liver benign neoplasm + 32
Path 2
Term Annotations click to browse term
  disease 12699
    disease of anatomical entity 12239
      gastrointestinal system disease 4073
        Digestive System Neoplasms 1810
          Gastrointestinal Neoplasms 1684
            gastrointestinal system benign neoplasm 139
              hepatobiliary benign neoplasm 109
                biliary tract benign neoplasm + 83
                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.