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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 5:106,865,192...106,865,746
Ensembl chr 5:106,865,192...106,865,746
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 chr 7:54,213,305...54,237,880
Ensembl chr 7:54,213,319...54,236,625
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 chr 1:219,076,618...219,126,221
Ensembl chr 1:219,077,771...219,126,220
JBrowse link
G F5 coagulation factor V IEP protein:increased expression:serum RGD PMID:25200834 RGD:10449102 NCBI chr13:82,479,997...82,535,540
Ensembl chr13:82,479,998...82,535,534
JBrowse link
G Rac1 Rac family small GTPase 1 ISO RGD PMID:12865273 RGD:13432048 NCBI chr12:13,090,316...13,111,841
Ensembl chr12:13,090,172...13,111,873
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 chr18:27,011,710...27,106,323
Ensembl chr18:27,047,382...27,105,531
JBrowse link
G Birc7 baculoviral IAP repeat-containing 7 ISO RGD PMID:21122381 RGD:13217408 NCBI chr 3:176,438,335...176,443,864
Ensembl chr 3:176,439,199...176,443,195
JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:8264230 RGD:13210753 NCBI chr 6:109,300,433...109,303,299
Ensembl chr 6:109,300,433...109,303,299
JBrowse link
G Gstm1 glutathione S-transferase mu 1 susceptibility ISO DNA:deletion:cds (human) RGD PMID:20375710 RGD:7495820 NCBI chr 2:210,803,869...210,809,461
Ensembl chr 2:210,803,869...210,809,306
JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO DNA:SNP: :p.A114V (human) RGD PMID:20375710 RGD:7495820 NCBI chr 1:219,291,679...219,294,147
Ensembl chr 1:219,291,679...219,294,147
JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:8264230 RGD:13210753 NCBI chr 5:114,011,184...114,014,277
Ensembl chr 5:114,011,189...114,014,277
JBrowse link
G Mapk8 mitogen-activated protein kinase 8 ISO RGD PMID:21122381, PMID:23082052 RGD:13217408, RGD:13217413 NCBI chr16:9,620,854...9,709,342
Ensembl chr16:9,625,177...9,709,347
JBrowse link
G Mir224 microRNA 224 ISO mRNA:increased expression:colorectal mucosa: RGD PMID:25919696 RGD:14398749 NCBI chr  X:152,223,754...152,223,835
Ensembl chr  X:152,223,754...152,223,835
JBrowse link
G Odc1 ornithine decarboxylase 1 ISO ClinVar Annotator: match by term: Colonic adenoma recurrence, reduced risk of ClinVar PMID:12810952 NCBI chr 6:42,852,529...42,859,142
Ensembl chr 6:42,852,683...42,859,927
JBrowse link
G Raf1 Raf-1 proto-oncogene, serine/threonine kinase ISO RGD PMID:21122381 RGD:13217408 NCBI chr 4:147,532,040...147,592,769
Ensembl chr 4:147,532,042...147,592,699
JBrowse link
G Smad4 SMAD family member 4 ISO mRNA:increased expression:mucosa RGD PMID:11480790 RGD:21066339 NCBI chr18:69,626,682...69,657,373
Ensembl chr18:69,627,757...69,671,199
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 4:157,864,905...157,877,634
Ensembl chr 4:157,864,969...157,877,633
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 1:221,704,394...221,710,343
Ensembl chr 1:221,704,493...221,710,331
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 chr18:27,011,710...27,106,323
Ensembl chr18:27,047,382...27,105,531
JBrowse link
G Cdkn1b cyclin-dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:15525823 NCBI chr 4:168,689,043...168,694,159
Ensembl chr 4:168,689,163...168,693,964
JBrowse link
G Egfr epidermal growth factor receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:16839708 NCBI chr14:99,919,485...100,104,136
Ensembl chr14:99,919,485...100,098,796
JBrowse link
G Fos Fos proto-oncogene, AP-1 transcription factor subunit ISO RGD PMID:21975339 RGD:13210759 NCBI chr 6:109,300,433...109,303,299
Ensembl chr 6:109,300,433...109,303,299
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 chr16:9,620,854...9,709,342
Ensembl chr16:9,625,177...9,709,347
JBrowse link
G Mcc MCC regulator of WNT signaling pathway ISO CTD Direct Evidence: marker/mechanism CTD PMID:8071957 NCBI chr18:35,683,185...35,817,117
NCBI chr 1:12,006,663...12,128,849
Ensembl chr 1:12,006,660...12,128,845
Ensembl chr18:12,006,660...12,128,845
JBrowse link
G Mthfr methylenetetrahydrofolate reductase severity ISO DNA:transition:cds:g.677C>T (human) RGD PMID:21865946 RGD:6893664 NCBI chr 5:164,844,642...164,864,360
Ensembl chr 5:164,845,925...164,860,910
JBrowse link
G Muc2 mucin 2, oligomeric mucus/gel-forming ISO CTD Direct Evidence: marker/mechanism CTD PMID:12468628 NCBI chr 1:214,663,929...214,693,197 JBrowse link
G Nras NRAS proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:3102434 NCBI chr 2:205,553,119...205,563,716
Ensembl chr 2:205,553,163...205,560,791
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 2:118,831,350...118,861,456
Ensembl chr 2:118,831,350...118,861,454
JBrowse link
G Pik3cb phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta disease_progression ISO RGD PMID:25473181 RGD:13432031 NCBI chr 8:107,275,849...107,381,088
Ensembl chr 8:107,275,725...107,380,933
JBrowse link
G Pmepa1 prostate transmembrane protein, androgen induced 1 ISO mRNA:increased expression:rectum RGD PMID:11568975 RGD:2315108 NCBI chr 3:171,295,630...171,342,662
Ensembl chr 3:171,294,856...171,342,646
JBrowse link
G Tyms thymidylate synthetase ISO CTD Direct Evidence: marker/mechanism CTD PMID:16931962 NCBI chr 9:121,918,875...121,931,564
Ensembl chr 9:121,918,947...121,931,564
JBrowse link
G Wrap53 WD repeat containing, antisense to TP53 treatment ISO RGD PMID:22805008 RGD:21081677 NCBI chr10:56,169,024...56,185,800
Ensembl chr10:56,169,025...56,185,857
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16035
    disease of anatomical entity 15289
      gastrointestinal system disease 4633
        intestinal disease 1515
          Intestinal Neoplasms 689
            intestinal benign neoplasm 31
              appendiceal neoplasm + 1
              cecal benign neoplasm + 0
              colonic benign neoplasm + 3
              colorectal adenoma 14
              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 16035
    disease of anatomical entity 15289
      gastrointestinal system disease 4633
        Gastrointestinal Diseases 2554
          Gastrointestinal Neoplasms 1771
            gastrointestinal system benign neoplasm 153
              intestinal benign neoplasm 31
                appendiceal neoplasm + 1
                cecal benign neoplasm + 0
                colonic benign neoplasm + 3
                colorectal adenoma 14
                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