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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
For additional species annotation, visit the Alliance of Genome Resources.



show annotations for term's descendants           Sort by:
 
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 chr18:26,463,333...26,465,531
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 JBrowse link
G Muc3 mucin 3, intestinal IEP mRNA:increased expression:bile duct RGD PMID:19032457 RGD:2325170 NCBI chr12:19,527,251...19,536,924 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 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
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
Nisch syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cldn1 claudin 1 ISO ClinVar Annotator: match by term: Neonatal ichthyosis-sclerosing cholangitis syndrome
DNA:deletion, nonsense mutation:exon:200_201delTT(human)
ClinVar Annotator: match by null
OMIM
ClinVar
RGD
PMID:12164927 PMID:15521008 PMID:16619213 PMID:25741868 PMID:15521008 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: Ichthyosis, leukocyte vacuoles, alopecia, and sclerosing cholangitis
ClinVar Annotator: match by term: Neonatal ichthyosis-sclerosing cholangitis syndrome
ClinVar PMID:12164927 PMID:15521008 PMID:16619213 PMID:25741868 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 ClinVar Annotator: match by term: SCLEROSING CHOLANGITIS, NEONATAL
ClinVar Annotator: match by term: Sclerosing cholangitis, neonatal
DNA:missense mutation, deletion:cds:p.K17N, p.F142_R186del (human)
ClinVar
RGD
PMID:25557784 PMID:25741868 PMID:27319779 PMID:27469900 PMID:28492532 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 17286
    disease of anatomical entity 16621
      gastrointestinal system disease 6080
        biliary tract disease 466
          bile duct disease 431
            cholangitis 32
              acute cholangitis 0
              ascending cholangitis 0
              autoimmune cholangitis 0
              cholecystitis + 1
              chronic cholangitis 1
              pericholangitis 0
              sclerosing cholangitis + 19
              suppurative cholangitis 0
Path 2
Term Annotations click to browse term
  disease 17286
    disease of anatomical entity 16621
      gastrointestinal system disease 6080
        hepatobiliary disease 2577
          biliary tract disease 466
            bile duct disease 431
              cholangitis 32
                acute cholangitis 0
                ascending cholangitis 0
                autoimmune cholangitis 0
                cholecystitis + 1
                chronic cholangitis 1
                pericholangitis 0
                sclerosing cholangitis + 19
                suppurative cholangitis 0
paths to the root