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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:cholangitis
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Accession:DOID:9446 term browser browse the term
Definition:A bile duct disease that is an inflammation of the bile duct. (DO)
Synonyms:exact_synonym: cholangitides
 primary_id: MESH:D002761
 xref: ICD9CM:576.1;   NCI:C26718


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cholangitis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb4 ATP binding cassette subfamily B member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:8698195 NCBI chr 4:25,150,998...25,209,489
Ensembl chr 4:25,151,953...25,209,202 		JBrowse link
G Car2 carbonic anhydrase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:15816485 NCBI chr 2:86,741,625...86,756,766
Ensembl chr 2:86,741,626...86,756,818 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 treatment IEP RGD PMID:17102917 RGD:14995925 NCBI chr10:67,005,424...67,007,222
Ensembl chr10:67,005,424...67,007,226 		JBrowse link
G Col1a1 collagen type I alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr10:79,883,622...79,900,625
Ensembl chr10:79,883,622...79,900,624 		JBrowse link
G Cxcl2 C-X-C motif chemokine ligand 2 treatment IEP RGD PMID:17102917 RGD:14995925 NCBI chr14:17,181,030...17,183,075
Ensembl chr14:17,181,062...17,183,075 		JBrowse link
G Egr1 early growth response 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr18:26,462,967...26,466,766
Ensembl chr18:26,462,981...26,466,766 		JBrowse link
G Itgb6 integrin subunit beta 6 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr 3:45,046,295...45,170,532
Ensembl chr 3:45,048,044...45,121,671 		JBrowse link
G Krt19 keratin 19 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr10:85,075,835...85,080,552
Ensembl chr10:85,066,802...85,171,799 		JBrowse link
G Muc3 mucin 3 IEP mRNA:increased expression:bile duct RGD PMID:19032457 RGD:2325170 NCBI chr12:19,527,251...19,536,924
Ensembl chr12:19,527,321...19,538,522 		JBrowse link
G Nras NRAS proto-oncogene, GTPase ISO mRNA:increased expression:cd4-positive helper T cells (human) RGD PMID:30690835 RGD:14975104 NCBI chr 2:190,582,885...190,593,509
Ensembl chr 2:190,582,918...190,591,626 		JBrowse link
G Pkhd1 PKHD1 ciliary IPT domain containing fibrocystin/polyductin ISO RGD PMID:29158418 RGD:14700923 NCBI chr 9:22,547,396...23,037,443
Ensembl chr 9:22,549,513...23,037,381 		JBrowse link
G Tgfb2 transforming growth factor, beta 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr13:98,160,075...98,261,771
Ensembl chr13:98,160,087...98,261,405 		JBrowse link
G Timp1 TIMP metallopeptidase inhibitor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr  X:1,212,969...1,217,714
Ensembl chr  X:1,212,972...1,217,664 		JBrowse link
G Tlr2 toll-like receptor 2 disease_progression ISO RGD PMID:30340822 RGD:15090860 NCBI chr 2:169,200,620...169,206,819
Ensembl chr 2:169,197,419...169,206,630 		JBrowse link
G Vdr vitamin D receptor ISO mRNA,protein:decreased expression:liver RGD PMID:28146070 RGD:14401745 NCBI chr 7:128,987,981...129,037,677
Ensembl chr 7:128,987,981...129,037,677 		JBrowse link
cholecystitis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb4 ATP binding cassette subfamily B member 4 ISS OMIM:600803 MouseDO NCBI chr 4:25,150,998...25,209,489
Ensembl chr 4:25,151,953...25,209,202 		JBrowse link
G Pot1 protection of telomeres 1 ISO mRNA:decreased expression:gall bladder RGD PMID:28643740 RGD:151356941 NCBI chr 4:54,205,330...54,263,137
Ensembl chr 4:54,205,332...54,263,042 		JBrowse link
chronic cholangitis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb4 ATP binding cassette subfamily B member 4 ISO RGD PMID:17852852 RGD:14694983 NCBI chr 4:25,150,998...25,209,489
Ensembl chr 4:25,151,953...25,209,202 		JBrowse link
ichthyosis, leukocyte vacuoles, alopecia, and sclerosing cholangitis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cldn1 claudin 1 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: CLDN1-related condition | ClinVar Annotator: match by term: Neonatal ichthyosis-sclerosing cholangitis syndrome
DNA:deletion, nonsense mutation:exon:200_201delTT(human)		 OMIM
CTD
ClinVar
RGD		 PMID:12164927 PMID:15521008 PMID:16619213 PMID:25741868 PMID:28492532 More... RGD:11341732 NCBI chr11:74,421,569...74,436,728
Ensembl chr11:74,421,569...74,436,724 		JBrowse link
G Cldn16 claudin 16 ISO ClinVar Annotator: match by term: CLDN1-related condition | ClinVar Annotator: match by term: Neonatal ichthyosis-sclerosing cholangitis syndrome ClinVar PMID:12164927 PMID:15521008 PMID:16619213 PMID:25741868 PMID:28492532 NCBI chr11:74,290,298...74,309,588
Ensembl chr11:74,290,298...74,309,588 		JBrowse link
primary sclerosing cholangitis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb4 ATP binding cassette subfamily B member 4 ISS OMIM:613806 MouseDO NCBI chr 4:25,150,998...25,209,489
Ensembl chr 4:25,151,953...25,209,202 		JBrowse link
G Cftr CF transmembrane conductance regulator susceptibility ISO associated with inflammatory bowel disease; DNA:misense mutations:multiple RGD PMID:12783301 RGD:25671445 NCBI chr 4:46,561,269...46,728,759
Ensembl chr 4:46,560,885...46,728,756 		JBrowse link
G Dnase1 deoxyribonuclease 1 ISO protein:decreased activity:serum (human) RGD PMID:28263100 RGD:38500241 NCBI chr10:11,498,930...11,505,151
Ensembl chr10:11,498,931...11,501,869 		JBrowse link
G Gnrhr gonadotropin releasing hormone receptor ISO mRNA:increased expression:liver: RGD PMID:28502477 RGD:14928320 NCBI chr14:21,856,871...21,874,861
Ensembl chr14:21,856,871...21,874,861 		JBrowse link
G Krt18 keratin 18 severity ISO protein:increased degradation:serum (human) RGD PMID:26195313 RGD:18337492 NCBI chr 7:133,157,486...133,161,162
Ensembl chr 7:133,157,475...133,161,166 		JBrowse link
G Mir155 microRNA 155 ISO miRNA:decreased expression:serum RGD PMID:30653586 RGD:21081530 NCBI chr11:23,774,654...23,774,718
Ensembl chr11:23,774,654...23,774,718 		JBrowse link
G Mir200b microRNA 200b treatment ISO RNA:increased expression:liver RGD PMID:28634212 PMID:28634212 RGD:14928323, RGD:14928323 NCBI chr 5:166,649,272...166,649,366
Ensembl chr 5:166,649,272...166,649,366 		JBrowse link
G RT1-Bb RT1 class II, locus Bb disease_progression ISO RGD PMID:30487703 RGD:14865010 NCBI chr20:4,596,558...4,602,201
Ensembl chr20:4,596,559...4,607,597 		JBrowse link
G Tnf tumor necrosis factor ISO protein:increased expression:serum (human) RGD PMID:9047083 RGD:14995307 NCBI chr20:3,622,011...3,624,629
Ensembl chr20:3,622,011...3,624,629 		JBrowse link
G Vdr vitamin D receptor ISO mRNA:decreased expression:liver RGD PMID:28146070 RGD:14401745 NCBI chr 7:128,987,981...129,037,677
Ensembl chr 7:128,987,981...129,037,677 		JBrowse link
G Vegfa vascular endothelial growth factor A ISO protein:increased expression:plasma: RGD PMID:26615570 RGD:11538286 NCBI chr 9:14,955,300...14,970,641
Ensembl chr 9:14,955,300...14,970,641 		JBrowse link
sclerosing cholangitis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb4 ATP binding cassette subfamily B member 4 ISO CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:16472600 PMID:29808285 PMID:15236191 RGD:14694980 NCBI chr 4:25,150,998...25,209,489
Ensembl chr 4:25,151,953...25,209,202 		JBrowse link
G Bcl2l11 Bcl2-like 11 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21151127 NCBI chr 3:115,366,783...115,404,068
Ensembl chr 3:115,366,646...115,404,068 		JBrowse link
G Dcdc2 doublecortin domain containing 2 ISO DNA:missense mutation, deletion:cds:p.K17N, p.F142_R186del (human)
ClinVar Annotator: match by term: Isolated neonatal sclerosing cholangitis
CTD Direct Evidence: marker/mechanism		 ClinVar
CTD
OMIM
RGD		 PMID:16199547 PMID:23677054 PMID:23746548 PMID:25557784 PMID:25741868 More... RGD:11568452 NCBI chr17:39,845,952...40,031,781
Ensembl chr17:39,845,952...40,030,743 		JBrowse link
G Hif1a hypoxia inducible factor 1 subunit alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:22271822 NCBI chr 6:92,624,059...92,669,262
Ensembl chr 6:92,624,390...92,669,261 		JBrowse link
G Mst1 macrophage stimulating 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21151127 NCBI chr 8:108,767,886...108,773,425
Ensembl chr 8:108,768,839...108,773,416 		JBrowse link
G Nos2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:12612912 NCBI chr10:63,815,308...63,851,208
Ensembl chr10:63,815,308...63,851,210 		JBrowse link
G Ubash3a ubiquitin associated and SH3 domain containing, A ISO CTD Direct Evidence: marker/mechanism CTD PMID:27992413 NCBI chr20:9,291,471...9,334,685
Ensembl chr20:9,292,139...9,329,224 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18969
    disease of anatomical entity 18249
      gastrointestinal system disease 7095
        hepatobiliary disease 3069
          biliary tract disease 540
            bile duct disease 496
              cholangitis 33
                acute cholangitis 0
                ascending cholangitis 0
                autoimmune cholangitis 0
                cholecystitis + 2
                chronic cholangitis 1
                pericholangitis 0
                sclerosing cholangitis + 19
                suppurative cholangitis 0
paths to the root