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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:intestinal benign neoplasm
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Accession:DOID:4610 term browser browse the term
Definition:A gastrointestinal system benign neoplasm that is located_in the intestine. (DO)
Synonyms:exact_synonym: intestinal tumors;   intestine growth;   neoplasm of intestinal tract
 xref: NCI:C3141
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 Ifnb1 interferon beta 1 ISO CTD Direct Evidence: therapeutic CTD PMID:12170190 PMID:12397731 NCBI chr 5:103,020,758...103,021,595
Ensembl chr 5:103,020,969...103,021,523 		JBrowse link
appendiceal neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Daxx death-domain associated protein ISO DNA:CNV: (human) RGD PMID:30962504 RGD:152025217 NCBI chr20:4,970,090...4,976,145
Ensembl chr20:4,970,092...4,975,843 		JBrowse link
G Nap1l1 nucleosome assembly protein 1-like 1 severity ISO mRNA:increased expression:appendix, mucosa (human) RGD PMID:16794389 RGD:9590083 NCBI chr 7:46,933,278...46,957,853
Ensembl chr 7:46,933,356...46,956,593 		JBrowse link
colon adenoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Axin2 axin 2 ISO protein:increased expression:: RGD PMID:11809809 RGD:151356508 NCBI chr10:93,893,830...93,927,042
Ensembl chr10:93,899,245...93,926,231 		JBrowse link
G Cacna1d calcium voltage-gated channel subunit alpha1 D ISO protein:increased expression:colon (human) RGD PMID:29079724 RGD:152177516 NCBI chr16:5,227,157...5,521,163
Ensembl chr16:5,228,306...5,668,215 		JBrowse link
G Ccnd1 cyclin D1 severity ISO RGD PMID:11375949 RGD:151665121 NCBI chr 1:200,089,002...200,098,524
Ensembl chr 1:200,089,002...200,098,602 		JBrowse link
G Ccnd2 cyclin D2 severity ISO RGD PMID:11375949 RGD:151665121 NCBI chr 4:159,966,883...159,989,261
Ensembl chr 4:159,962,363...159,989,495 		JBrowse link
G Chka choline kinase alpha ISO protein:increased expression:colonic mucosa (human) RGD PMID:10363580 RGD:10401945 NCBI chr 1:201,076,804...201,125,517
Ensembl chr 1:201,076,860...201,125,516 		JBrowse link
G Igf2bp1 insulin-like growth factor 2 mRNA binding protein 1 ISO RGD PMID:26194191 RGD:11086893 NCBI chr10:80,908,300...80,951,097
Ensembl chr10:80,908,076...80,951,129 		JBrowse link
G Rac1 Rac family small GTPase 1 ISO RGD PMID:12865273 RGD:13432048 NCBI chr12:11,037,028...11,057,251
Ensembl chr12:11,036,698...11,057,251 		JBrowse link
G Rbp4 retinol binding protein 4 ISO protein:increased expression:blood serum (human) RGD PMID:25712946 RGD:329849123 NCBI chr 1:235,893,917...235,901,315
Ensembl chr 1:235,893,917...235,901,399 		JBrowse link
G Tet2 tet methylcytosine dioxygenase 2 ISO mRNA:decreased expression:colon (human) RGD PMID:29875879 RGD:150429665 NCBI chr 2:221,988,645...222,072,813
Ensembl chr 2:221,988,645...222,072,534 		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:11823972 PMID:11904335 More... NCBI chr18:25,828,558...25,925,511
Ensembl chr18:25,864,222...25,922,696 		JBrowse link
G Birc7 baculoviral IAP repeat-containing 7 ISO RGD PMID:21122381 RGD:13217408 NCBI chr 3:168,047,824...168,052,606
Ensembl chr 3:168,047,824...168,052,606 		JBrowse link
G Cyp24a1 cytochrome P450, family 24, subfamily a, polypeptide 1 severity
treatment		 ISO DNA:SNPs:intron, CDS: (rs927650), (rs35051736) (human)
DNA:SNP:CDS: (rs2296241) (human)		 RGD PMID:26241700 PMID:27978548 RGD:11521055, RGD:152025254 NCBI chr 3:159,275,947...159,290,383
Ensembl chr 3:159,275,947...159,290,383 		JBrowse link
G Ezh2 enhancer of zeste 2 polycomb repressive complex 2 subunit disease_progression ISO protein:increased expression:large intestine RGD PMID:30214616 RGD:126779593 NCBI chr 4:76,624,399...76,687,362
Ensembl chr 4:76,624,399...76,687,362 		JBrowse link
G F5 coagulation factor V ISO protein:increased expression:serum RGD PMID:30971492 RGD:40907058 NCBI chr13:76,513,509...76,583,106
Ensembl chr13:76,513,255...76,582,317 		JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:8264230 RGD:13210753 NCBI chr 6:105,121,170...105,124,036
Ensembl chr 6:105,121,170...105,124,036 		JBrowse link
G Gpx2 glutathione peroxidase 2 ISO mRNA:increased expression:colorectum (human) RGD PMID:30469315 RGD:151665806 NCBI chr 6:95,493,589...95,496,877
Ensembl chr 6:95,493,589...95,496,877 		JBrowse link
G Gpx3 glutathione peroxidase 3 ISO mRNA:decreased expression:colorectum (human) RGD PMID:30469315 RGD:151665806 NCBI chr10:39,028,624...39,036,695
Ensembl chr10:39,028,570...39,037,035 		JBrowse link
G Gstm1 glutathione S-transferase mu 1 susceptibility ISO DNA:deletion:cds (human) RGD PMID:20375710 RGD:7495820 NCBI chr 2:195,649,845...195,655,402
Ensembl chr 2:195,649,845...195,655,411 		JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO DNA:SNP: :p.A114V (human) RGD PMID:20375710 RGD:7495820 NCBI chr 1:201,337,762...201,340,230
Ensembl chr 1:201,321,672...201,340,226 		JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:8264230 RGD:13210753 NCBI chr 5:109,894,175...109,897,268
Ensembl chr 5:109,893,145...109,897,656 		JBrowse link
G Map2k4 mitogen activated protein kinase kinase 4 ISO protein:decreased expression:colorectum (human) RGD PMID:28423721 RGD:150429743 NCBI chr10:50,343,227...50,447,956
Ensembl chr10:50,344,915...50,447,993 		JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO RGD PMID:21122381 PMID:23082052 RGD:13217408, RGD:13217413 NCBI chr16:8,638,897...8,721,960
Ensembl chr16:8,638,924...8,721,981 		JBrowse link
G Mir193b microRNA 193b disease_progression ISO RNA:decreased expression:blood plasma (human) RGD PMID:29226653 RGD:153344556 NCBI chr10:1,317,742...1,317,824
Ensembl chr10:1,317,742...1,317,824 		JBrowse link
G Mir224 microRNA 224 ISO mRNA:increased expression:colorectal mucosa: RGD PMID:25919696 RGD:14398749 NCBI chr  X:150,065,088...150,065,169
Ensembl chr  X:150,065,088...150,065,169 		JBrowse link
G Myd88 MYD88, innate immune signal transduction adaptor ameliorates ISO RGD PMID:30063920 RGD:150519915 NCBI chr 8:119,074,439...119,078,508
Ensembl chr 8:119,074,437...119,079,415 		JBrowse link
G Ptch1 patched 1 ISO RGD PMID:24612059 RGD:150523840 NCBI chr17:1,542,705...1,607,730
Ensembl chr17:1,542,877...1,607,333 		JBrowse link
G Ptgis prostaglandin I2 synthase susceptibility ISO DNA:repeats:promoter: RGD PMID:16537708 RGD:151347835 NCBI chr 3:155,928,564...155,964,228
Ensembl chr 3:155,916,412...155,965,451 		JBrowse link
G Raf1 Raf-1 proto-oncogene, serine/threonine kinase ISO RGD PMID:21122381 RGD:13217408 NCBI chr 4:148,679,534...148,740,265
Ensembl chr 4:148,679,530...148,740,317 		JBrowse link
G Selenoh selenoprotein H ISO mRNA:increased expression:colorectum (human) RGD PMID:30469315 RGD:151665806 NCBI chr 3:69,751,850...69,753,417
Ensembl chr 3:69,752,757...69,753,417 		JBrowse link
G Selenop selenoprotein P ISO mRNA:decreased expression:colorectum (human) RGD PMID:30469315 RGD:151665806 NCBI chr 2:52,498,123...52,508,409
Ensembl chr 2:52,498,339...52,508,852 		JBrowse link
G Selenos selenoprotein S ISO mRNA:decreased expression:colorectum (human) RGD PMID:30469315 RGD:151665806 NCBI chr 1:119,659,779...119,669,546
Ensembl chr 1:119,659,751...119,669,833 		JBrowse link
G Sephs2 selenophosphate synthetase 2 ISO mRNA:decreased expression:colorectum (human) RGD PMID:30469315 RGD:151665806 NCBI chr 1:181,893,146...181,895,464
Ensembl chr 1:181,892,599...181,895,497 		JBrowse link
G Smad4 SMAD family member 4 ISO mRNA:increased expression:mucosa RGD PMID:11480790 RGD:21066339 NCBI chr18:67,243,742...67,274,438
Ensembl chr18:67,243,742...67,274,438 		JBrowse link
G Smarcc1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 ameliorates ISO protein:increased expression:colorectal mucosa (human) RGD PMID:19156145 RGD:151347861 NCBI chr 8:110,111,097...110,214,734
Ensembl chr 8:110,111,122...110,214,720 		JBrowse link
G Tnfrsf1a TNF receptor superfamily member 1A ISO protein:increased expression:serum, colorectal mucosa, epithelial cell RGD PMID:23082052 RGD:13217413 NCBI chr 4:158,150,815...158,163,592
Ensembl chr 4:158,150,820...158,163,591 		JBrowse link
G Ttr transthyretin ISO protein:decreased expression:blood serum (human)
protein:decreased expression:colorectum (human)		 RGD PMID:21136704 PMID:33739034 RGD:151664608, RGD:151660505 NCBI chr18:11,941,791...11,951,008
Ensembl chr18:11,943,789...11,951,008 		JBrowse link
G Txnrd3 thioredoxin reductase 3 ISO mRNA:increased expression:colorectum (human) RGD PMID:30469315 RGD:151665806 NCBI chr 4:122,072,548...122,112,493
Ensembl chr 4:122,072,548...122,112,491 		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 chr 1:203,638,905...203,644,871
Ensembl chr 1:203,639,000...203,644,871 		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 chr18:25,828,558...25,925,511
Ensembl chr18:25,864,222...25,922,696 		JBrowse link
G Cdkn1b cyclin-dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:15525823 NCBI chr 4:167,760,067...167,765,177
Ensembl chr 4:167,760,181...167,764,982 		JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:16839708 NCBI chr14:91,176,979...91,349,722
Ensembl chr14:91,177,067...91,344,382 		JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:21975339 RGD:13210759 NCBI chr 6:105,121,170...105,124,036
Ensembl chr 6:105,121,170...105,124,036 		JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO DNA:SNP: :rs10508901 (human)
DNA:SNP: :rs10857561 (human)		 RGD PMID:22199996 PMID:23027623 RGD:13217410, RGD:13217411 NCBI chr16:8,638,897...8,721,960
Ensembl chr16:8,638,924...8,721,981 		JBrowse link
G Mcc MCC regulator of WNT signaling pathway ISO CTD Direct Evidence: marker/mechanism CTD PMID:8071957 NCBI chr18:36,794,206...37,266,237
Ensembl chr18:36,798,372...37,266,819 		JBrowse link
G Mthfr methylenetetrahydrofolate reductase severity ISO DNA:transition:cds:g.677C>T (human) RGD PMID:21865946 RGD:6893664 NCBI chr 5:158,465,248...158,484,999
Ensembl chr 5:158,465,296...158,483,797 		JBrowse link
G Muc2 mucin 2, oligomeric mucus/gel-forming ISO CTD Direct Evidence: marker/mechanism CTD PMID:12468628 NCBI chr 1:196,799,494...196,831,740
Ensembl chr 1:196,799,517...196,831,756 		JBrowse link
G Nras NRAS proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:3102434 NCBI chr 2:190,582,885...190,593,509
Ensembl chr 2:190,582,918...190,591,626 		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 chr 2:115,175,275...115,249,034
Ensembl chr 2:115,174,984...115,249,032 		JBrowse link
G Pik3cb phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta disease_progression ISO RGD PMID:25473181 RGD:13432031 NCBI chr 8:99,594,600...99,699,772
Ensembl chr 8:99,594,644...99,699,663 		JBrowse link
G Pmepa1 prostate transmembrane protein, androgen induced 1 ISO mRNA:increased expression:rectum RGD PMID:11568975 RGD:2315108 NCBI chr 3:162,011,884...162,060,343
Ensembl chr 3:162,012,751...162,060,454 		JBrowse link
G Tyms thymidylate synthetase ISO CTD Direct Evidence: marker/mechanism CTD PMID:16931962 NCBI chr 9:113,313,454...113,329,551
Ensembl chr 9:113,313,452...113,329,536 		JBrowse link
G Wrap53 WD repeat containing, antisense to TP53 treatment ISO RGD PMID:22805008 RGD:21081677 NCBI chr10:54,282,092...54,299,908
Ensembl chr10:54,282,105...54,298,929 		JBrowse link
sigmoid 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 ClinVar Annotator: match by term: Sigmoid colon cancer ClinVar PMID:25741868 PMID:28492532 NCBI chr18:25,828,558...25,925,511
Ensembl chr18:25,864,222...25,922,696 		JBrowse link
G Msh2 mutS homolog 2 ISO ClinVar Annotator: match by term: Sigmoid colon cancer ClinVar PMID:10495924 PMID:12658575 PMID:15849733 PMID:17312306 PMID:18566915 More... NCBI chr 6:6,813,793...6,872,960
Ensembl chr 6:6,813,795...6,872,938 		JBrowse link
G Msh6 mutS homolog 6 ISO ClinVar Annotator: match by term: Sigmoid colon cancer ClinVar PMID:9354786 PMID:12376507 PMID:18809606 PMID:19924528 PMID:20176959 More... NCBI chr 6:6,562,631...6,579,995
Ensembl chr 6:6,562,632...6,579,956 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 21128
    disease of anatomical entity 18211
      gastrointestinal system disease 7050
        Gastrointestinal Neoplasms 3711
          gastrointestinal system benign neoplasm 236
            intestinal benign neoplasm 56
              appendiceal neoplasm + 2
              cecal benign neoplasm + 0
              colonic benign neoplasm + 12
              colorectal adenoma 30
              intestinal neuroendocrine benign tumor + 1
              large bowel leiomyoma + 0
              large intestine adenoma 0
              large intestine lipoma + 0
              rectal benign neoplasm + 15
              small intestine benign neoplasm + 1
Path 2
Term Annotations click to browse term
  disease 21128
    disease of cellular proliferation 7667
      Neoplasms by Site 7121
        Digestive System Neoplasms 3836
          Gastrointestinal Neoplasms 3711
            gastrointestinal system benign neoplasm 236
              intestinal benign neoplasm 56
                appendiceal neoplasm + 2
                cecal benign neoplasm + 0
                colonic benign neoplasm + 12
                colorectal adenoma 30
                intestinal neuroendocrine benign tumor + 1
                large bowel leiomyoma + 0
                large intestine adenoma 0
                large intestine lipoma + 0
                rectal benign neoplasm + 15
                small intestine benign neoplasm + 1
paths to the root