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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:gastrointestinal system benign neoplasm
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Accession:DOID:0050624 term browser browse the term
Definition:An organ system benign neoplasm located_in gastrointestinal tract organs. (DO)
For additional species annotation, visit the Alliance of Genome Resources.


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anus benign neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101968765 interferon beta ISO CTD Direct Evidence: therapeutic CTD PMID:12170190, PMID:12397731 NCBI chrNW_004936652:2,736,270...2,736,833 JBrowse link
appendiceal neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Nap1l1 nucleosome assembly protein 1 like 1 severity ISO mRNA:increased expression:appendix, mucosa (human) RGD PMID:16794389 RGD:9590083 NCBI chrNW_004936568:4,416,225...4,440,566 JBrowse link
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 chrNW_004936592:4,728,371...4,833,830 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 chrNW_004936493:10,509,118...10,549,144 JBrowse link
G Apoe apolipoprotein E susceptibility ISO DNA:SNP:intron:rs440446 (human) RGD PMID:18296645 RGD:2317550 NCBI chrNW_004936706:1,512,438...1,516,805 JBrowse link
G Tjp1 tight junction protein 1 ISO protein:decreased expression:bile duct RGD PMID:19184677 RGD:2325030 NCBI chrNW_004936483:1,814,870...2,045,802 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 chrNW_004936496:11,604,992...11,815,680 JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chrNW_004936678:365,005...560,546 JBrowse link
G Fscn1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile duct RGD PMID:17419223 RGD:2317786 NCBI chrNW_004936765:609,894...619,417 JBrowse link
G Met MET proto-oncogene, receptor tyrosine kinase ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15892172 RGD:2317585 NCBI chrNW_004936589:2,280,803...2,390,179 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 chrNW_004936486:16,744,607...16,923,209 JBrowse link
G Mki67 marker of proliferation Ki-67 disease_progression ISO RGD PMID:9869516 RGD:2317706 NCBI chrNW_004936486:15,561,327...15,587,109 JBrowse link
G Muc16 mucin 16, cell surface associated ISO protein:increased expression:serum,bile RGD PMID:1657243 RGD:2325134 NCBI chrNW_004936588:5,506,683...5,586,450 JBrowse link
G Muc4 mucin 4, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:16857800 RGD:2324929 NCBI chrNW_004936784:515,608...539,915 JBrowse link
G Ncam1 neural cell adhesion molecule 1 disease_progression ISO RGD PMID:8501910, PMID:9851639 RGD:2326076, RGD:2326077 NCBI chrNW_004936612:1,262,557...1,556,281 JBrowse link
G Runx3 RUNX family transcription factor 3 ISO DNA:hypermethylation:promoter RGD PMID:15471559 RGD:2324957 NCBI chrNW_004936474:9,751,946...9,802,910 JBrowse link
biliary tract benign neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ctps1 CTP synthase 1 ISO mRNA:increased expression:biliary tract neoplasm (human) RGD PMID:12819026 RGD:2317903 NCBI chrNW_004936474:22,611,037...22,633,208 JBrowse link
G Elf3 E74 like ETS transcription factor 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936567:2,494,645...2,500,361 JBrowse link
G Faslg Fas ligand ISO associated with Biliary Tract Disease;protein:decreased expression:serum RGD PMID:15138553, PMID:15287856 RGD:2317742, RGD:2317743 NCBI chrNW_004936481:14,789,547...14,795,780 JBrowse link
G Hgf hepatocyte growth factor ISO mRNA:increased expression: : RGD PMID:12819026 RGD:2317903 NCBI chrNW_004936734:354,798...428,356 JBrowse link
G Il4 interleukin 4 ISO RGD PMID:18798553 RGD:2317263 NCBI chrNW_004936647:2,510,457...2,518,576 JBrowse link
G Mdm2 MDM2 proto-oncogene ISO protein:increased expression:biliary epithelium (human) RGD PMID:16505435 RGD:2317415 NCBI chrNW_004936545:6,709,903...6,732,334 JBrowse link
G Mtap methylthioadenosine phosphorylase ISO RGD PMID:16373701 RGD:2317953 NCBI chrNW_004936652:3,431,588...3,468,770 JBrowse link
G Muc1 mucin 1, cell surface associated ISO RGD PMID:19129927 RGD:2317987 NCBI chrNW_004936580:4,691,870...4,694,092 JBrowse link
G Muc4 mucin 4, cell surface associated ISO protein:increased expression:bile,biliary tract RGD PMID:18475301 RGD:2324916 NCBI chrNW_004936784:515,608...539,915 JBrowse link
G Muc5ac mucin 5AC, oligomeric mucus/gel-forming disease_progression ISO protein:increased expression:serum RGD PMID:18475301 RGD:2324916 NCBI chrNW_004936816:129,926...159,396 JBrowse link
G Prkacb protein kinase cAMP-activated catalytic subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936608:1,353,905...1,464,636 JBrowse link
cholangiocarcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcc2 ATP binding cassette subfamily C member 2 susceptibility ISO DNA:polymorphism:exon:c.3972C>T (human) RGD PMID:19451719 RGD:2317508 NCBI chrNW_004936636:292,631...341,999 JBrowse link
G Adrb2 adrenoceptor beta 2 ISO protein:decreased expression:liver RGD PMID:16292515 RGD:2325640 NCBI chrNW_004936504:5,985,407...5,987,453 JBrowse link
G Alox5 arachidonate 5-lipoxygenase ISO protein:increased expression:bile duct RGD PMID:18507031 RGD:2317521 NCBI chrNW_004936554:7,807,914...7,848,691 JBrowse link
G Anxa2 annexin A2 disease_progression ISO RGD PMID:20493868 RGD:2325728 NCBI chrNW_004936471:21,274,112...21,329,286 JBrowse link
G Apc APC regulator of WNT signaling pathway ISO DNA:loss of heterozygosity
DNA:hypermethylation:promoter
RGD PMID:10212000, PMID:15467712 RGD:2317198, RGD:2317205 NCBI chrNW_004936531:6,899,580...7,019,016 JBrowse link
G Apoa1 apolipoprotein A1 ISO protein:decreased expression:serum RGD PMID:19486127 RGD:2325756 NCBI chrNW_004936542:2,111,055...2,112,626 JBrowse link
G Arid1a AT-rich interaction domain 1A ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936474:11,148,857...11,197,312 JBrowse link
G Asph aspartate beta-hydroxylase ISO RGD PMID:21898484 RGD:6902945 NCBI chrNW_004936496:11,604,992...11,815,680 JBrowse link
G Bap1 BRCA1 associated protein 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509, PMID:25231345 NCBI chrNW_004936473:3,239,009...3,247,806 JBrowse link
G Braf B-Raf proto-oncogene, serine/threonine kinase ISO DNA:missense mutation:cds:p.V600E (human) RGD PMID:12692057 RGD:11073239 NCBI chrNW_004936592:4,728,371...4,833,830 JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: therapeutic CTD PMID:17341899 NCBI chrNW_004936678:365,005...560,546 JBrowse link
G Epo erythropoietin ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chrNW_004936543:742,722...745,332 JBrowse link
G Epor erythropoietin receptor ISO mRNA, protein:increased expression:liver RGD PMID:23052842 RGD:10400912 NCBI chrNW_004936659:1,468,391...1,473,880 JBrowse link
G Erbb2 erb-b2 receptor tyrosine kinase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635 NCBI chrNW_004936490:14,887,062...14,910,038 JBrowse link
G Faslg Fas ligand ISO RGD PMID:11029528 RGD:2317746 NCBI chrNW_004936481:14,789,547...14,795,780 JBrowse link
G Fgf2 fibroblast growth factor 2 ISO protein:increased expression:bile RGD PMID:11478488 RGD:2317765 NCBI chrNW_004936662:1,886,176...1,928,998 JBrowse link
G Fgfr2 fibroblast growth factor receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936486:10,506,680...10,606,272 JBrowse link
G Fscn1 fascin actin-bundling protein 1 disease_progression ISO protein:increased expression:bile ducts RGD PMID:19721413 RGD:2317780 NCBI chrNW_004936765:609,894...619,417 JBrowse link
G 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 chrNW_004936530:1,353,432...1,407,437 JBrowse link
G Gstp1 glutathione S-transferase pi 1 treatment ISO human cell line in a mouse model
DNA:hypermethylation:promoter
RGD PMID:12805482, PMID:15467712 RGD:14401711, RGD:2317198 NCBI chrNW_004936599:2,197,681...2,200,642 JBrowse link
G Hdac6 histone deacetylase 6 ISO protein:increased expression:liver: RGD PMID:23370327 RGD:9681560 NCBI chrNW_004936721:757,500...778,416 JBrowse link
G Hgf hepatocyte growth factor ISO mRNA, protein:increased expression: :
protein:increased expression:serum
RGD PMID:10827151, PMID:16974053 RGD:2317909, RGD:2317925 NCBI chrNW_004936734:354,798...428,356 JBrowse link
G Idh1 isocitrate dehydrogenase (NADP(+)) 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936950:334,894...349,221 JBrowse link
G Idh2 isocitrate dehydrogenase (NADP(+)) 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936483:15,845,777...15,864,341 JBrowse link
G Il4r interleukin 4 receptor ISO mRNA:increased expression:bile duct RGD PMID:18798553 RGD:2317263 NCBI chrNW_004936501:11,025,590...11,058,807 JBrowse link
G Kmt2c lysine methyltransferase 2C ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936527:7,310,885...7,508,032 JBrowse link
G Kras KRAS proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8968066, PMID:22561520 NCBI chrNW_004936548:2,078,568...2,113,877 JBrowse link
G Krt7 keratin 7 ISO RGD PMID:18393293 RGD:2317308 NCBI chrNW_004936512:9,641,587...9,656,573 JBrowse link
G LOC101967357 mucin-6 ISO protein:increased expression: : RGD PMID:10209489 RGD:2325167 NCBI chrNW_004936816:882...14,717 JBrowse link
G Mdm2 MDM2 proto-oncogene disease_progression ISO protein:increased expression:intrahepatic bile duct (human) RGD PMID:15619210 RGD:2317417 NCBI chrNW_004936545:6,709,903...6,732,334 JBrowse link
G Met MET proto-oncogene, receptor tyrosine kinase disease_progression ISO protein:increased phosphorylation:liver, carcinoma (human)
protein:increased expression:liver, biliary epithelium (rat)
RGD PMID:14656942, PMID:16818635 RGD:2317578, RGD:2317601 NCBI chrNW_004936589:2,280,803...2,390,179 JBrowse link
G Mgmt O-6-methylguanine-DNA methyltransferase ISO DNA:hypermethylation:promoter (human) RGD PMID:17550320 RGD:2317632 NCBI chrNW_004936486:16,744,607...16,923,209 JBrowse link
G Mki67 marker of proliferation Ki-67 disease_progression ISO RGD PMID:12903495 RGD:2317705 NCBI chrNW_004936486:15,561,327...15,587,109 JBrowse link
G Mmp2 matrix metallopeptidase 2 disease_progression ISO protein:increased expression:bile duct RGD PMID:15213623, PMID:19629755 RGD:2324667, RGD:2325769 NCBI chrNW_004936475:7,801,356...7,825,831 JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO protein:increased expression:bile duct
mRNA:increased expression:bile duct
RGD PMID:15213623, PMID:16463672 RGD:2324667, RGD:2325856 NCBI chrNW_004936514:7,038,240...7,045,873 JBrowse link
G Mthfr methylenetetrahydrofolate reductase susceptibility ISO DNA:polymorphism (human) RGD PMID:17201138 RGD:2317119 NCBI chrNW_004936474:623,438...637,849 JBrowse link
G Muc1 mucin 1, cell surface associated disease_progression ISO protein:increased secretion:bile
protein:increased expression:bile duct:
protein:increased expression:serum
mRNA:increased expression:bile duct
RGD PMID:15213623, PMID:18081149, PMID:19055478, PMID:19260467, PMID:19639217 RGD:2317986, RGD:2324622, RGD:2324638, RGD:2324664, RGD:2324667 NCBI chrNW_004936580:4,691,870...4,694,092 JBrowse link
G Muc16 mucin 16, cell surface associated ISO associated with Opisthorchiasis;protein:increased expression:serum RGD PMID:1653472 RGD:2325142 NCBI chrNW_004936588:5,506,683...5,586,450 JBrowse link
G Muc2 mucin 2, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chrNW_004936816:60,499...91,628 JBrowse link
G Muc3a mucin 3A, cell surface associated ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chrNW_004936543:886,333...904,504 JBrowse link
G Muc4 mucin 4, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:14752841, PMID:19082442 RGD:2303602, RGD:2324944 NCBI chrNW_004936784:515,608...539,915 JBrowse link
G Muc5ac mucin 5AC, oligomeric mucus/gel-forming disease_progression ISO protein:increased expression:serum
mRNA:increased expression:bile duct
RGD PMID:11680592, PMID:14508831 RGD:2324948, RGD:2324990 NCBI chrNW_004936816:129,926...159,396 JBrowse link
G Muc5b mucin 5B, oligomeric mucus/gel-forming ISO mRNA:decreased expression:bile duct RGD PMID:11680592 RGD:2324948 NCBI chrNW_004936816:174,943...209,241 JBrowse link
G Ncam1 neural cell adhesion molecule 1 ISO associated with hepatitis RGD PMID:12031086 RGD:2326079 NCBI chrNW_004936612:1,262,557...1,556,281 JBrowse link
G Nos2 nitric oxide synthase 2 ISO protein:increased expression:bile duct
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:16094703, PMID:16818635 RGD:2325280 NCBI chrNW_004936538:4,052,277...4,097,051 JBrowse link
G Notch1 notch receptor 1 ISO protein:increased expression:cholangiocyte RGD PMID:15887117 RGD:2325330 NCBI chrNW_004936669:1,292,016...1,334,061 JBrowse link
G Nr1h4 nuclear receptor subfamily 1 group H member 4 disease_progression ISO mRNA:decreased expression:liver (rat) RGD PMID:24255171 RGD:15090822 NCBI chrNW_004936492:13,315,265...13,365,186 JBrowse link
G Ogg1 8-oxoguanine DNA glycosylase disease_progression ISO DNA:loss of heterozygosity (human) RGD PMID:11260864, PMID:11866974 RGD:2317134, RGD:2317136 NCBI chrNW_004936602:3,411,106...3,418,826 JBrowse link
G Pawr pro-apoptotic WT1 regulator ISO mRNA,protein:decreased expression:cholangiocyte: RGD PMID:20724592 RGD:9835357 NCBI chrNW_004936698:650,225...746,593 JBrowse link
G Pbrm1 polybromo 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24185509 NCBI chrNW_004936473:3,382,618...3,476,049 JBrowse link
G Peg3 paternally expressed 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936882:577,424...607,691 JBrowse link
G Prkaca protein kinase cAMP-activated catalytic subunit alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936659:2,750,015...2,765,914 JBrowse link
G Prkacb protein kinase cAMP-activated catalytic subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:26258846 NCBI chrNW_004936608:1,353,905...1,464,636 JBrowse link
G Pten phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:23376645, PMID:27022031 RGD:12802341 NCBI chrNW_004936735:1,252,414...1,338,318 JBrowse link
G Ptgs2 prostaglandin-endoperoxide synthase 2 ISO protein:increased expression:bile duct
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:16818635, PMID:19621664 RGD:2317180 NCBI chrNW_004936481:3,821,564...3,828,086 JBrowse link
G Reg1a regenerating family member 1 alpha susceptibility ISO mRNA, protein:increased expression:liver (human) RGD PMID:11343228 RGD:10044031 NCBI chrNW_004936556:4,873,331...4,875,608 JBrowse link
G Rnf43 ring finger protein 43 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936490:4,660,904...4,742,669 JBrowse link
G Robo2 roundabout guidance receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936505:5,544,011...6,747,417 JBrowse link
G Runx3 RUNX family transcription factor 3 ISO protein:decreased expression:bile duct RGD PMID:19827872 RGD:2324955 NCBI chrNW_004936474:9,751,946...9,802,910 JBrowse link
G Slc5a5 solute carrier family 5 member 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17408651 NCBI chrNW_004936596:3,176,009...3,188,637 JBrowse link
G Smad4 SMAD family member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22561520 NCBI chrNW_004936497:12,242,869...12,278,012 JBrowse link
G Sox17 SRY-box transcription factor 17 severity ISO RGD PMID:20816680 RGD:4889598 NCBI chrNW_004936496:1,248,582...1,251,406 JBrowse link
G Tgfb1 transforming growth factor beta 1 disease_progression ISO protein:increased expression:pancreas RGD PMID:12632524, PMID:16083599 RGD:1299231, RGD:2325020 NCBI chrNW_004936661:3,742,080...3,758,266 JBrowse link
G Tgfbr2 transforming growth factor beta receptor 2 ISO mRNA:increased expression:bile duct RGD PMID:12632524 RGD:1299231 NCBI chrNW_004936473:21,324,669...21,409,430 JBrowse link
G Thbs1 thrombospondin 1 disease_progression ISO DNA:hypermethylation (human) RGD PMID:11927969, PMID:12213730, PMID:16465407 RGD:2325024, RGD:2325026, RGD:2325027 NCBI chrNW_004936471:3,064,466...3,081,125 JBrowse link
G Tnc tenascin C severity ISO RGD PMID:20816680 RGD:4889598 NCBI chrNW_004936487:4,172,263...4,256,780 JBrowse link
G Tp53 tumor protein p53 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16818635, PMID:22561520 NCBI chrNW_004936595:919,807...935,367 JBrowse link
colon adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Chka choline kinase alpha ISO protein:increased expression:colonic mucosa (human) RGD PMID:10363580 RGD:10401945 NCBI chrNW_004936599:2,031,953...2,068,423 JBrowse link
G F5 coagulation factor V ISO protein:increased expression:serum RGD PMID:25200834 RGD:10449102 NCBI chrNW_004936481:17,114,441...17,178,902 JBrowse link
G Rac1 Rac family small GTPase 1 ISO RGD PMID:12865273 RGD:13432048 NCBI chrNW_004936750:107,689...122,679 JBrowse link
colorectal adenoma 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: Colorectal adenoma ClinVar PMID:2472832, PMID:10811618, PMID:11257105, PMID:11904335, PMID:16454848, PMID:18199528, PMID:18844223, PMID:20233475, PMID:21859464, PMID:22703879, PMID:22722839, PMID:22995991, PMID:23085758, PMID:23292937, PMID:23970361, PMID:24033266, PMID:24055113, PMID:24728327, PMID:24861525, PMID:25178641, PMID:25203624, PMID:25318351, PMID:25479140, PMID:25559809, PMID:25637381, PMID:25741868, PMID:25778705, PMID:25980754, PMID:26332594, PMID:26416840, PMID:26467025, PMID:26580448, PMID:27153395, PMID:27535533, PMID:27600092, PMID:28301460, PMID:28492532, PMID:28503720, PMID:28873162, PMID:29212164, PMID:30256826, PMID:30311386 NCBI chrNW_004936531:6,899,580...7,019,016 JBrowse link
G Birc7 baculoviral IAP repeat containing 7 ISO RGD PMID:21122381 RGD:13217408 NCBI chrNW_004936514:10,618,347...10,622,906 JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:8264230 RGD:13210753 NCBI chrNW_004936488:4,384,710...4,388,118 JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO DNA:SNP: :p.A114V (human) RGD PMID:20375710 RGD:7495820 NCBI chrNW_004936599:2,197,681...2,200,642 JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:8264230 RGD:13210753 NCBI chrNW_004936522:3,034,364...3,037,632 JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO RGD PMID:21122381, PMID:23082052 RGD:13217408, RGD:13217413 NCBI chrNW_004936728:1,775,746...1,893,895 JBrowse link
G Odc1 ornithine decarboxylase 1 ISO ClinVar Annotator: match by term: Colonic adenoma recurrence, reduced risk of ClinVar PMID:12810952 NCBI chrNW_004936532:6,581,717...6,587,116 JBrowse link
G Raf1 Raf-1 proto-oncogene, serine/threonine kinase ISO RGD PMID:21122381 RGD:13217408 NCBI chrNW_004936602:1,089,979...1,114,376 JBrowse link
G Smad4 SMAD family member 4 ISO mRNA:increased expression:mucosa RGD PMID:11480790 RGD:21066339 NCBI chrNW_004936497:12,242,869...12,278,012 JBrowse link
G Tnfrsf1a TNF receptor superfamily member 1A ISO protein:increased expression:serum, colorectal mucosa, epithelial cell RGD PMID:23082052 RGD:13217413 NCBI chrNW_004936709:1,407,327...1,421,448 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 chrNW_004936493:10,509,118...10,549,144 JBrowse link
G Fscn1 fascin actin-bundling protein 1 ISO mRNA, protein:increased expression: : RGD PMID:15136764 RGD:2317789 NCBI chrNW_004936765:609,894...619,417 JBrowse link
G Mtap methylthioadenosine phosphorylase ISO DNA, protein:deletion, decreased expression:common bile duct: RGD PMID:15662124 RGD:2317954 NCBI chrNW_004936652:3,431,588...3,468,770 JBrowse link
G Muc1 mucin 1, cell surface associated disease_progression ISO protein:increased expression:bile duct RGD PMID:8766528 RGD:2324856 NCBI chrNW_004936580:4,691,870...4,694,092 JBrowse link
G Muc4 mucin 4, cell surface associated ISO protein:increased expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chrNW_004936784:515,608...539,915 JBrowse link
G Muc5ac mucin 5AC, oligomeric mucus/gel-forming ISO protein:altered expression:pancreas RGD PMID:8143972 RGD:2324890 NCBI chrNW_004936816:129,926...159,396 JBrowse link
G Tymp thymidine phosphorylase disease_progression ISO RGD PMID:10760693 RGD:2325158 NCBI chrNW_004936629:315,609...320,356 JBrowse link
duodenal gastrinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Men1 menin 1 ISO associated with Neuroendocrine Tumors; DNA:loss of heterozygosity: : RGD PMID:17135306 RGD:2317341 NCBI chrNW_004936599:4,504,489...4,510,085 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 chrNW_004936668:62,103...81,549 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 associated with tuberous sclerosis;DNA:mutations:multiple RGD PMID:22251200, PMID:29512829 RGD:21079730, RGD:21079732 NCBI chrNW_004936694:1,958,152...1,993,373 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
RGD
CTD
PMID:15509519 RGD:1358261 NCBI chrNW_004936870:424,832...468,303 JBrowse link
G Carm1 coactivator associated arginine methyltransferase 1 ISO mRNA,protein:increased expression:liver: RGD PMID:23912631 RGD:9586718 NCBI chrNW_004936659:1,071,883...1,120,917 JBrowse link
G Cdkn1b cyclin dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:17620307 NCBI chrNW_004936587:4,573,166...4,578,480 JBrowse link
G Ctnnb1 catenin beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21147764 NCBI chrNW_004936473:29,999,542...30,034,610 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 chrNW_004936668:62,103...81,549 JBrowse link
G Hras HRas proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8200073 NCBI chrNW_004936888:375,372...378,125 JBrowse link
G Kras KRAS proto-oncogene, GTPase induced ISO aflatoxin B1 induced:DNA:transversion,transition mutations:cds: RGD PMID:8446626 RGD:11568697 NCBI chrNW_004936548:2,078,568...2,113,877 JBrowse link
G LOC101971161 ubiquitin-conjugating enzyme E2 E2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chrNW_004936473:14,988,802...15,280,650 JBrowse link
G LOC101973029 cytochrome P450 2E1 treatment ISO RGD PMID:23543859 RGD:14700918 NCBI chrNW_004936486:19,691,822...19,702,684 JBrowse link
G LOC101976500 haptoglobin ISO RGD PMID:10569800 RGD:1626391 NCBI chrNW_004936475:21,841,054...21,845,821 JBrowse link
G Mki67 marker of proliferation Ki-67 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31939706 NCBI chrNW_004936486:15,561,327...15,587,109 JBrowse link
G Nr1h4 nuclear receptor subfamily 1 group H member 4 ISO RGD PMID:17183066 RGD:14696794 NCBI chrNW_004936492:13,315,265...13,365,186 JBrowse link
G Nr1i3 nuclear receptor subfamily 1 group I member 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25656644 NCBI chrNW_004936903:527,838...533,930 JBrowse link
G Pten phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:15199412, PMID:27022031 RGD:1302555 NCBI chrNW_004936735:1,252,414...1,338,318 JBrowse link
G Tmem70 transmembrane protein 70 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chrNW_004936648:2,636,667...2,650,311 JBrowse link
insulinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Adm adrenomedullin ISO protein:increased expression:pancreas, plasma RGD PMID:11331218 RGD:2325319 NCBI chrNW_004936528:8,005,223...8,007,586 JBrowse link
G Btc betacellulin ISO protein:increased expression:pancreas RGD PMID:10724350 RGD:2326087 NCBI chrNW_004936598:971,253...1,019,043 JBrowse link
G Cd40 CD40 molecule ISO RGD PMID:17982058 RGD:5491180 NCBI chrNW_004936514:6,936,915...6,947,246 JBrowse link
G Cxcl12 C-X-C motif chemokine ligand 12 ISO protein:increased expression:pancreas RGD PMID:19013212 RGD:2317608 NCBI chrNW_004936617:4,224,131...4,239,080 JBrowse link
G Ins insulin ISO protein:altered localization:pancreas
protein:altered expression:blood
RGD PMID:2565624, PMID:8175958 RGD:2317266, RGD:2317268 NCBI chrNW_004936816:1,002,137...1,003,357 JBrowse link
G Men1 menin 1 disease_progression ISO DNA:deletion:exon
ClinVar Annotator: match by term: Insulinoma
CTD Direct Evidence: marker/mechanism
DNA:deletions:exons
RGD
ClinVar
CTD
PMID:12941803, PMID:17961653, PMID:19208834, PMID:20138042, PMID:25741868, PMID:30311386 RGD:2317288, RGD:2317292, RGD:2317310 NCBI chrNW_004936599:4,504,489...4,510,085 JBrowse link
G Ncam1 neural cell adhesion molecule 1 ISO protein:increased expression:pancreas RGD PMID:8972754 RGD:2326080 NCBI chrNW_004936612:1,262,557...1,556,281 JBrowse link
G Rps15 ribosomal protein S15 ISO RGD PMID:3019805 RGD:61740 NCBI chrNW_004936588:762,153...763,405 JBrowse link
G Slc2a2 solute carrier family 2 member 2 ISO protein:increased expression:pancreatic B cell
mRNA:decreased expression:pancreatic islet
RGD PMID:8421107, PMID:12114701 RGD:2324976, RGD:2324977 NCBI chrNW_004936593:1,572,661...1,605,071 JBrowse link
G Tgfa transforming growth factor alpha ISO protein:increased expression:pancreas RGD PMID:8712689 RGD:2317472 NCBI chrNW_004936491:14,659,089...14,758,614 JBrowse link
G Tgfb1 transforming growth factor beta 1 ISO mRNA, protein:decreased expression:pancreatic islet RGD PMID:18058603 RGD:2325017 NCBI chrNW_004936661:3,742,080...3,758,266 JBrowse link
intrahepatic cholangiocarcinoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apc APC regulator of WNT signaling pathway ISO ClinVar Annotator: match by term: Intrahepatic Cholangiocarcinoma ClinVar PMID:24728327, PMID:25479140, PMID:25741868, PMID:26530882, PMID:28492532 NCBI chrNW_004936531:6,899,580...7,019,016 JBrowse link
G Arid1a AT-rich interaction domain 1A disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chrNW_004936474:11,148,857...11,197,312 JBrowse link
G Becn1 beclin 1 disease_progression ISO RGD PMID:30849962 RGD:14974231 NCBI chrNW_004936490:17,518,100...17,531,126 JBrowse link
G Braf B-Raf proto-oncogene, serine/threonine kinase severity ISO DNA:missense mutation:cds:p.V600E (human) RGD PMID:24139215 RGD:14398746 NCBI chrNW_004936592:4,728,371...4,833,830 JBrowse link
G Fas Fas cell surface death receptor disease_progression ISO RGD PMID:11003620 RGD:14700701 NCBI chrNW_004936735:209,369...234,582 JBrowse link
G Faslg Fas ligand severity ISO RGD PMID:11003620 RGD:14700701 NCBI chrNW_004936481:14,789,547...14,795,780 JBrowse link
G Foxp3 forkhead box P3 ISO DNA:hypomethylation:liver RGD PMID:24291052 RGD:38599002 NCBI chrNW_004936721:1,118,376...1,125,282 JBrowse link
G Idh1 isocitrate dehydrogenase (NADP(+)) 1 no_association ISO DNA:misssense mutations:cds:p.Arg132Cys,Arg132Leu (human) RGD PMID:26245674 RGD:14974229 NCBI chrNW_004936950:334,894...349,221 JBrowse link
G Idh2 isocitrate dehydrogenase (NADP(+)) 2 disease_progression ISO DNA:mutations: : RGD PMID:22824796 RGD:14985256 NCBI chrNW_004936483:15,845,777...15,864,341 JBrowse link
G Kras KRAS proto-oncogene, GTPase disease_progression ISO DNA:mutations:: RGD PMID:24139215 RGD:14398746 NCBI chrNW_004936548:2,078,568...2,113,877 JBrowse link
G Smad4 SMAD family member 4 disease_progression ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866, PMID:23981608 RGD:18936999, RGD:21066336 NCBI chrNW_004936497:12,242,869...12,278,012 JBrowse link
Klatskin's tumor term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apc APC regulator of WNT signaling pathway ISO ClinVar Annotator: match by term: Klatskin tumor ClinVar PMID:25741868 NCBI chrNW_004936531:6,899,580...7,019,016 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 chrNW_004936524:9,584,302...9,592,961 JBrowse link
G Cbx7 chromobox 7 ISO RGD PMID:22214847 RGD:9587356 NCBI chrNW_004936492:2,411,171...2,428,484 JBrowse link
G Cdkn1a cyclin dependent kinase inhibitor 1A ISO protein:increased expression:liver RGD PMID:23890812 RGD:13792775 NCBI chrNW_004936476:22,717,308...22,725,127 JBrowse link
G Col1a1 collagen type I alpha 1 chain onset ISO mRNA:increased expression:liver (rat) RGD PMID:21295105 RGD:5130894 NCBI chrNW_004936490:11,448,552...11,465,836 JBrowse link
G Eif4g2 eukaryotic translation initiation factor 4 gamma 2 ISO RGD PMID:9633945 RGD:10755510 NCBI chrNW_004936528:7,563,965...7,574,630 JBrowse link
G Hspa4 heat shock protein family A (Hsp70) member 4 ISO protein:increased expression:liver (rat) RGD PMID:22213170 RGD:5686872 NCBI chrNW_004936647:2,087,650...2,133,343 JBrowse link
G Il10 interleukin 10 treatment ISO RGD PMID:25168696 RGD:11049493 NCBI chrNW_004936557:5,834,874...5,838,502 JBrowse link
G Kmt5c lysine methyltransferase 5C disease_progression ISO protein:decreased expression:liver RGD PMID:16497704 RGD:9586726 NCBI chrNW_004936886:596,949...602,959 JBrowse link
G LOC101966907 histone H2AX treatment ISO RGD PMID:23474136 RGD:8693737 NCBI chrNW_004936542:4,046,930...4,049,017 JBrowse link
G Map2k3 mitogen-activated protein kinase kinase 3 ISO RGD PMID:24233520 RGD:7495808 NCBI chrNW_004936741:362,682...386,633 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 chrNW_004936589:2,280,803...2,390,179 JBrowse link
G Mthfr methylenetetrahydrofolate reductase onset ISO mRNA:decreased expression:liver (rat) RGD PMID:22213190 RGD:6893663 NCBI chrNW_004936474:623,438...637,849 JBrowse link
G Nqo1 NAD(P)H quinone dehydrogenase 1 ISO RGD PMID:24418717 RGD:11035219 NCBI chrNW_004936475:19,771,384...19,785,034 JBrowse link
G Ttpa alpha tocopherol transfer protein ISO mRNA:decreased expression:liver RGD PMID:9178827 RGD:1600436 NCBI chrNW_004936496:10,409,948...10,466,722 JBrowse link
G Tut4 terminal uridylyl transferase 4 ISO human cells in a mouse model RGD PMID:24056962 RGD:11530012 NCBI chrNW_004936522:8,468,092...8,560,453 JBrowse link
pancreatic mucinous cystadenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Kras KRAS proto-oncogene, GTPase severity ISO DNA:mutations:cds: RGD PMID:28570009 RGD:14398747 NCBI chrNW_004936548:2,078,568...2,113,877 JBrowse link
pleomorphic adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Plag1 PLAG1 zinc finger ISO RGD PMID:10029085 RGD:1599086 NCBI chrNW_004936496:2,809,878...2,855,515 JBrowse link
Pleomorphic Salivary Gland Adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Plag1 PLAG1 zinc finger ISO OMIM NCBI chrNW_004936496:2,809,878...2,855,515 JBrowse link
rectal benign neoplasm 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 CTD Direct Evidence: marker/mechanism CTD PMID:8071957, PMID:11766074 NCBI chrNW_004936531:6,899,580...7,019,016 JBrowse link
G Cdkn1b cyclin dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:15525823 NCBI chrNW_004936587:4,573,166...4,578,480 JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:16839708 NCBI chrNW_004936678:365,005...560,546 JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:21975339 RGD:13210759 NCBI chrNW_004936488:4,384,710...4,388,118 JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO DNA:SNP: :rs10857561 (human)
DNA:SNP: :rs10508901 (human)
RGD PMID:22199996, PMID:23027623 RGD:13217410, RGD:13217411 NCBI chrNW_004936728:1,775,746...1,893,895 JBrowse link
G Mcc MCC regulator of WNT signaling pathway ISO CTD Direct Evidence: marker/mechanism CTD PMID:8071957 NCBI chrNW_004936597:4,930,065...5,191,311 JBrowse link
G Mthfr methylenetetrahydrofolate reductase severity ISO DNA:transition:cds:g.677C>T (human) RGD PMID:21865946 RGD:6893664 NCBI chrNW_004936474:623,438...637,849 JBrowse link
G Muc2 mucin 2, oligomeric mucus/gel-forming ISO CTD Direct Evidence: marker/mechanism CTD PMID:12468628 NCBI chrNW_004936816:60,499...91,628 JBrowse link
G Nras NRAS proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:3102434 NCBI chrNW_004936627:73,413...82,590 JBrowse link
G Pik3ca phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha susceptibility ISO DNA:SNP:intron: (rs7651265) (human) RGD PMID:20622004 RGD:5685669 NCBI chrNW_004936566:3,924,013...3,951,052 JBrowse link
G Pik3cb phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta disease_progression ISO RGD PMID:25473181 RGD:13432031 NCBI chrNW_004936540:907,118...1,041,814 JBrowse link
G Pmepa1 prostate transmembrane protein, androgen induced 1 ISO mRNA:increased expression:rectum RGD PMID:11568975 RGD:2315108 NCBI chrNW_004936530:429,059...439,847 JBrowse link
G Tyms thymidylate synthetase ISO CTD Direct Evidence: marker/mechanism CTD PMID:16931962 NCBI chrNW_004936550:33,797...42,233 JBrowse link
G Wrap53 WD repeat containing antisense to TP53 treatment ISO RGD PMID:22805008 RGD:21081677 NCBI chrNW_004936595:936,184...952,784 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 11962
    disease of cellular proliferation 5201
      Neoplasms by Site 4631
        organ system benign neoplasm 409
          gastrointestinal system benign neoplasm 132
            appendix leiomyoma 0
            esophageal lipoma 0
            esophagus leiomyoma 0
            esophagus squamous cell papilloma 0
            gastric hemangioma 0
            gastric leiomyoma 0
            gastric teratoma + 0
            gastrointestinal adenoma 0
            gastrointestinal neuroendocrine benign tumor + 0
            hepatobiliary benign neoplasm + 103
            intestinal benign neoplasm + 27
            lipoadenoma 0
            pancreatic cystadenoma + 12
            pancreatic intraductal papillary-mucinous adenoma 0
            pleomorphic adenoma + 1
            squamous papillomatosis 0
Path 2
Term Annotations click to browse term
  disease 11962
    disease of anatomical entity 11526
      gastrointestinal system disease 3786
        Digestive System Neoplasms 1721
          Gastrointestinal Neoplasms 1590
            gastrointestinal system benign neoplasm 132
              appendix leiomyoma 0
              esophageal lipoma 0
              esophagus leiomyoma 0
              esophagus squamous cell papilloma 0
              gastric hemangioma 0
              gastric leiomyoma 0
              gastric teratoma + 0
              gastrointestinal adenoma 0
              gastrointestinal neuroendocrine benign tumor + 0
              hepatobiliary benign neoplasm + 103
              intestinal benign neoplasm + 27
              lipoadenoma 0
              pancreatic cystadenoma + 12
              pancreatic intraductal papillary-mucinous adenoma 0
              pleomorphic adenoma + 1
              squamous papillomatosis 0
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.