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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:liver benign neoplasm
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Accession:DOID:916 term browser browse the term
Definition:Tumors or cancer of the LIVER.
Synonyms:exact_synonym: epithelial hepatic and intrahepatic bile duct neoplasm
 xref: NCI:C7103;   NCI:C7106
For additional species annotation, visit the Alliance of Genome Resources.


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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 IEP protein:increased activity:liver (rat) RGD PMID:8264573 RGD:2313432 NCBI chr 5:64,805,772...64,818,813
Ensembl chr 5:64,805,773...64,818,824
JBrowse link
G Apobec1 apolipoprotein B mRNA editing enzyme catalytic subunit 1 IMP RGD PMID:9633945 RGD:10755510 NCBI chr 4:155,386,367...155,414,034
Ensembl chr 4:155,386,711...155,401,480
JBrowse link
G Cbx7 chromobox 7 ISO RGD PMID:22214847 RGD:9587356 NCBI chr 7:121,136,067...121,153,503
Ensembl chr 7:121,136,058...121,153,383
JBrowse link
G Cdkn1a cyclin-dependent kinase inhibitor 1A IEP protein:increased expression:liver RGD PMID:23890812 RGD:13792775 NCBI chr20:6,348,422...6,358,864
Ensembl chr20:6,351,458...6,358,864
JBrowse link
G Col1a1 collagen type I alpha 1 chain onset IEP mRNA:increased expression:liver (rat) RGD PMID:21295105 RGD:5130894 NCBI chr10:82,745,801...82,762,790
Ensembl chr10:82,745,801...82,762,789
JBrowse link
G Eif4g2 eukaryotic translation initiation factor 4, gamma 2 ISO RGD PMID:9633945 RGD:10755510 NCBI chr 1:175,883,362...175,895,510
Ensembl chr 1:175,883,363...175,895,510
JBrowse link
G H2ax H2A.X variant histone treatment IEP RGD PMID:23474136 RGD:8693737 NCBI chr 8:48,665,652...48,666,981
Ensembl chr 8:48,665,652...48,666,981
JBrowse link
G Hspa4 heat shock protein family A (Hsp70) member 4 IEP protein:increased expression:liver (rat) RGD PMID:22213170 RGD:5686872 NCBI chr10:38,601,624...38,642,397
Ensembl chr10:38,601,624...38,642,397
JBrowse link
G Il10 interleukin 10 treatment IEP RGD PMID:25168696 RGD:11049493 NCBI chr13:47,738,933...47,743,392
Ensembl chr13:47,739,526...47,743,392
JBrowse link
G Kmt5c lysine methyltransferase 5C disease_progression IEP protein:decreased expression:liver RGD PMID:16497704 RGD:9586726 NCBI chr 1:72,666,662...72,674,271
Ensembl chr 1:72,666,665...72,674,271
JBrowse link
G Map2k3 mitogen activated protein kinase kinase 3 ISO RGD PMID:24233520 RGD:7495808 NCBI chr10:45,089,455...45,110,802
Ensembl chr10:47,182,433...47,203,753
JBrowse link
G Met MET proto-oncogene, receptor tyrosine kinase onset IEP mRNA, protein:increased expression:neoplastic liver (rat) RGD PMID:11956651 RGD:2317546 NCBI chr 4:44,747,467...44,854,628
Ensembl chr 4:44,774,741...44,852,665
JBrowse link
G Mthfr methylenetetrahydrofolate reductase onset IEP mRNA:decreased expression:liver (rat) RGD PMID:22213190 RGD:6893663 NCBI chr 5:164,844,642...164,864,360
Ensembl chr 5:164,845,925...164,860,910
JBrowse link
G Nqo1 NAD(P)H quinone dehydrogenase 1 IEP RGD PMID:24418717 RGD:11035219 NCBI chr19:38,422,210...38,437,103
Ensembl chr19:38,422,164...38,437,180
JBrowse link
G Ttpa alpha tocopherol transfer protein IEP mRNA:decreased expression:liver RGD PMID:9178827 RGD:1600436 NCBI chr 5:34,007,926...34,029,315
Ensembl chr 5:34,007,920...34,028,452
JBrowse link
G Tut4 terminal uridylyl transferase 4 ISO human cells in a mouse model RGD PMID:24056962 RGD:11530012 NCBI chr 5:128,063,880...128,168,726
Ensembl chr 5:128,083,118...128,168,207
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 ClinVar Annotator: match by term: Hepatic adenomas, familial ClinVar
OMIM
PMID:8866553, PMID:8945470, PMID:9032114, PMID:9045858, PMID:9075818, PMID:9166684, PMID:9313763, PMID:9392505, PMID:9439666, PMID:10333057, PMID:10447526, PMID:10754480, PMID:11058894, PMID:11315851, PMID:12050210, PMID:12355088, PMID:12530534, PMID:12574234, PMID:12618559, PMID:15649945, PMID:15928245, PMID:17054605, PMID:17407387, PMID:17440016, PMID:17573900, PMID:17937063, PMID:17989309, PMID:18414213, PMID:18672310, PMID:21051477, PMID:21628466, PMID:23551881, PMID:23607861, PMID:25174781, PMID:26467025 NCBI chr12:47,407,811...47,433,342
Ensembl chr12:47,407,811...47,433,342
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 IAGP DNA:mutations:multiple
associated with tuberous sclerosis;DNA:mutations:multiple
RGD PMID:29512829, PMID:22251200 RGD:21079730, RGD:21079732 NCBI chr10:13,962,006...13,996,684
Ensembl chr10:13,961,947...13,996,584
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 IEP
ISO
mRNA,protein:increased expression:liver:
CTD Direct Evidence: marker/mechanism
CTD PMID:15509519, PMID:15509519 RGD:1358261 NCBI chr 4:154,309,426...154,359,138
Ensembl chr 4:154,309,426...154,359,137
JBrowse link
G Carm1 coactivator-associated arginine methyltransferase 1 IEP mRNA,protein:increased expression:liver: RGD PMID:23912631 RGD:9586718 NCBI chr 8:22,577,723...22,622,555
Ensembl chr 8:22,577,715...22,622,560
JBrowse link
G Cdkn1b cyclin-dependent kinase inhibitor 1B ISO CTD Direct Evidence: marker/mechanism CTD PMID:17620307 NCBI chr 4:168,689,043...168,694,159
Ensembl chr 4:168,689,163...168,693,964
JBrowse link
G Ctnnb1 catenin beta 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21147764 NCBI chr 8:129,601,511...129,628,378
Ensembl chr 8:129,617,812...129,627,372
JBrowse link
G Cyp2e1 cytochrome P450, family 2, subfamily e, polypeptide 1 treatment IEP RGD PMID:23543859 RGD:14700918 NCBI chr 1:213,511,892...213,522,195
Ensembl chr 1:213,511,874...213,535,542
JBrowse link
G Cyp3a23-3a1 cytochrome P450, family 3, subfamily a, polypeptide 23-polypeptide 1 EXP CTD Direct Evidence: marker/mechanism CTD PMID:10959800 NCBI chr12:11,053,888...11,082,742
Ensembl chr12:11,655,402...11,733,136
JBrowse link
G Hnf1a HNF1 homeobox A susceptibility IAGP DNA:loss of heterozygosity, mutations:multiple
DNA:frameshift mutation, non-sense mutation:cds:R229X, G55fsX57 (human)
RGD PMID:12355088, PMID:14598263 RGD:14700683, RGD:14700774 NCBI chr12:47,407,811...47,433,342
Ensembl chr12:47,407,811...47,433,342
JBrowse link
G Hp haptoglobin IEP RGD PMID:10569800 RGD:1626391 NCBI chr19:42,096,255...42,100,805
Ensembl chr19:42,097,995...42,100,804
JBrowse link
G Hras HRas proto-oncogene, GTPase ISO CTD Direct Evidence: marker/mechanism CTD PMID:8200073 NCBI chr 1:214,178,404...214,181,841
Ensembl chr 1:214,178,407...214,181,686
JBrowse link
G Kras KRAS proto-oncogene, GTPase induced IAGP aflatoxin B1 induced:DNA:transversion,transition mutations:cds: RGD PMID:8446626 RGD:11568697 NCBI chr 4:179,482,562...179,515,483
Ensembl chr 4:179,486,105...179,515,558
JBrowse link
G Mki67 marker of proliferation Ki-67 ISO CTD Direct Evidence: marker/mechanism CTD PMID:31939706 NCBI chr 1:207,993,895...208,020,454
Ensembl chr 1:207,993,895...208,020,454
JBrowse link
G Nr1h4 nuclear receptor subfamily 1, group H, member 4 ISO RGD PMID:17183066 RGD:14696794 NCBI chr 7:30,003,429...30,162,095
Ensembl chr 7:30,003,429...30,162,056
JBrowse link
G Nr1i3 nuclear receptor subfamily 1, group I, member 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25656644 NCBI chr13:89,585,072...89,591,278
Ensembl chr13:89,586,283...89,591,277
JBrowse link
G Pten phosphatase and tensin homolog ISO CTD Direct Evidence: marker/mechanism CTD PMID:27022031, PMID:15199412 RGD:1302555 NCBI chr 1:251,421,814...251,487,634
Ensembl chr 1:251,421,596...251,487,832
JBrowse link
G Ptpn11 protein tyrosine phosphatase, non-receptor type 11 ISS MouseDO NCBI chr12:40,895,515...40,955,999
Ensembl chr12:40,895,515...40,955,999
JBrowse link
G Tmem70 transmembrane protein 70 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr 5:2,019,852...2,037,038
Ensembl chr 5:2,019,852...2,037,038
JBrowse link
G Ube2e2 ubiquitin-conjugating enzyme E2E 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:27914986 NCBI chr15:7,402,210...7,928,320
Ensembl chr15:7,871,497...7,927,939
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16023
    disease of cellular proliferation 5918
      Neoplasms by Site 5283
        Liver Neoplasms 952
          liver benign neoplasm 34
            Pascual Castroviejo Syndrome 0
            hemangioma of liver 0
            hepatic angiomyolipoma 1
            hepatocellular adenoma + 17
            liver fibroma 0
            liver leiomyoma 0
            liver lipoma 0
Path 2
Term Annotations click to browse term
  disease 16023
    disease of anatomical entity 15278
      gastrointestinal system disease 4632
        Digestive System Neoplasms 1911
          Gastrointestinal Neoplasms 1771
            gastrointestinal system benign neoplasm 153
              hepatobiliary benign neoplasm 121
                liver benign neoplasm 34
                  Pascual Castroviejo Syndrome 0
                  hemangioma of liver 0
                  hepatic angiomyolipoma 1
                  hepatocellular adenoma + 17
                  liver fibroma 0
                  liver leiomyoma 0
                  liver lipoma 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.