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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 4:22,133,984...22,192,687
Ensembl chr 4:22,133,521...22,425,515
JBrowse link
G Car2 carbonic anhydrase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:15816485 NCBI chr 2:88,097,740...88,112,868
Ensembl chr 2:88,097,720...88,113,029
JBrowse link
G Ccl2 C-C motif chemokine ligand 2 treatment IEP RGD PMID:17102917 RGD:14995925 NCBI chr10:69,412,065...69,413,863
Ensembl chr10:69,412,017...69,413,870
JBrowse link
G Col1a1 collagen type I alpha 1 chain ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr10:82,745,801...82,762,790
Ensembl chr10:82,745,801...82,762,789
JBrowse link
G Cxcl2 C-X-C motif chemokine ligand 2 treatment IEP RGD PMID:17102917 RGD:14995925 NCBI chr14:18,731,346...18,733,391
Ensembl chr14:18,731,378...18,733,391
JBrowse link
G Egr1 early growth response 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr18:27,657,903...27,660,101
Ensembl chr18:27,657,628...27,661,429
JBrowse link
G Itgb6 integrin subunit beta 6 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr 3:46,652,624...46,775,362
Ensembl chr 3:46,652,623...46,726,958
JBrowse link
G Krt19 keratin 19 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr10:88,055,843...88,060,560
Ensembl chr10:88,055,841...88,060,561
JBrowse link
G Muc3 mucin 3, intestinal IEP mRNA:increased expression:bile duct RGD PMID:19032457 RGD:2325170 NCBI chr12:22,535,663...22,584,775 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 2:205,553,119...205,563,716
Ensembl chr 2:205,553,163...205,560,791
JBrowse link
G Pkhd1 PKHD1 ciliary IPT domain containing fibrocystin/polyductin ISO RGD PMID:29158418 RGD:14700923 NCBI chr 9:26,164,969...26,736,704 JBrowse link
G Tgfb2 transforming growth factor, beta 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr13:105,039,639...105,142,010
Ensembl chr13:105,039,853...105,141,030
JBrowse link
G Timp1 TIMP metallopeptidase inhibitor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25055964 NCBI chr  X:1,364,771...1,369,451
Ensembl chr  X:1,364,786...1,369,384
JBrowse link
G Tlr2 toll-like receptor 2 disease_progression ISO RGD PMID:30340822 RGD:15090860 NCBI chr 2:182,840,171...182,846,061
Ensembl chr 2:182,840,727...182,846,061
JBrowse link
G Vdr vitamin D receptor ISO mRNA,protein:decreased expression:liver RGD PMID:28146070 RGD:14401745 NCBI chr 7:139,344,452...139,394,138
Ensembl chr 7:139,342,063...139,394,166
JBrowse link
acalculous 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 ISO ClinVar Annotator: match by term: Acalculous cholecystitis ClinVar PMID:17726488, PMID:18482588, PMID:19584064, PMID:23533021, PMID:25741868, PMID:25807286 NCBI chr 4:22,133,984...22,192,687
Ensembl chr 4:22,133,521...22,425,515
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 4:22,133,984...22,192,687
Ensembl chr 4:22,133,521...22,425,515
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 4:22,133,984...22,192,687
Ensembl chr 4:22,133,521...22,425,515
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 DNA:deletion, nonsense mutation:exon:200_201delTT(human)
ClinVar Annotator: match by null
OMIM
ClinVar
PMID:12164927, PMID:15521008, PMID:16619213, PMID:15521008 RGD:11341732 NCBI chr11:77,815,216...77,830,373
Ensembl chr11:77,815,181...77,830,416
JBrowse link
G Cldn16 claudin 16 ISO ClinVar Annotator: match by term: Ichthyosis, leukocyte vacuoles, alopecia, and sclerosing cholangitis ClinVar PMID:12164927, PMID:15521008, PMID:16619213 NCBI chr11:77,683,942...77,703,232
Ensembl chr11:77,681,794...77,703,255
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 4:22,133,984...22,192,687
Ensembl chr 4:22,133,521...22,425,515
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 4:42,693,263...42,860,679
Ensembl chr 4:42,692,836...42,860,676
JBrowse link
G Dnase1 deoxyribonuclease 1 ISO protein:decreased activity:serum (human) RGD PMID:28263100 RGD:38500241 NCBI chr10:11,757,681...11,760,672
Ensembl chr10:11,757,682...11,760,620
JBrowse link
G Gnrhr gonadotropin releasing hormone receptor ISO mRNA:increased expression:liver: RGD PMID:28502477 RGD:14928320 NCBI chr14:23,480,462...23,498,450
Ensembl chr14:23,480,462...23,498,450
JBrowse link
G Krt18 keratin 18 severity ISO protein:increased degradation:serum (human) RGD PMID:26195313 RGD:18337492 NCBI chr 7:143,629,455...143,633,131
Ensembl chr 7:143,629,455...143,633,131
JBrowse link
G Mir155 microRNA 155 ISO miRNA:decreased expression:serum RGD PMID:30653586 RGD:21081530 NCBI chr11:24,176,603...24,176,667
Ensembl chr11:24,176,603...24,176,667
JBrowse link
G Mir200b microRNA 200b treatment ISO RNA:increased expression:liver RGD PMID:28634212, PMID:28634212 RGD:14928323, RGD:14928323 NCBI chr 5:173,490,144...173,490,238
Ensembl chr 5:173,490,144...173,490,238
JBrowse link
G RT1-Bb RT1 class II, locus Bb disease_progression ISO RGD PMID:30487703 RGD:14865010 NCBI chr20:4,043,726...4,049,367
Ensembl chr20:4,039,413...4,049,711
JBrowse link
G Tnf tumor necrosis factor ISO protein:increased expression:serum (human) RGD PMID:9047083 RGD:14995307 NCBI chr20:5,189,382...5,192,000
Ensembl chr20:5,189,390...5,192,000
JBrowse link
G Vdr vitamin D receptor ISO mRNA:decreased expression:liver RGD PMID:28146070 RGD:14401745 NCBI chr 7:139,344,452...139,394,138
Ensembl chr 7:139,342,063...139,394,166
JBrowse link
G Vegfa vascular endothelial growth factor A ISO protein:increased expression:plasma: RGD PMID:26615570 RGD:11538286 NCBI chr 9:17,340,341...17,355,681
Ensembl chr 9:17,340,341...17,355,681
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 PMID:16472600, PMID:29808285, PMID:15236191 RGD:14694980 NCBI chr 4:22,133,984...22,192,687
Ensembl chr 4:22,133,521...22,425,515
JBrowse link
G Bcl2l11 BCL2 like 11 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21151127 NCBI chr 3:120,726,906...120,764,192
Ensembl chr 3:120,726,906...120,764,192
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 PMID:25557784, PMID:25741868, PMID:27319779, PMID:27469900, PMID:28492532, PMID:27319779 RGD:11568452 NCBI chr17:41,838,201...42,031,265
Ensembl chr17:41,838,201...42,031,265
JBrowse link
G Hif1a hypoxia inducible factor 1 subunit alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:22271822 NCBI chr 6:96,810,868...96,856,303
Ensembl chr 6:96,810,907...96,856,052
JBrowse link
G Mst1 macrophage stimulating 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21151127 NCBI chr 8:116,857,716...116,862,286
Ensembl chr 8:116,857,684...116,862,423
JBrowse link
G Nos2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:12612912 NCBI chr10:66,188,290...66,221,621
Ensembl chr10:66,189,786...66,313,190
JBrowse link
G Ubash3a ubiquitin associated and SH3 domain containing, A ISO CTD Direct Evidence: marker/mechanism CTD PMID:27992413 NCBI chr20:9,941,102...9,986,012
Ensembl chr20:9,948,908...9,985,133
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16108
    disease of anatomical entity 15356
      gastrointestinal system disease 4673
        biliary tract disease 437
          bile duct disease 407
            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 16108
    disease of anatomical entity 15356
      gastrointestinal system disease 4673
        hepatobiliary disease 2486
          biliary tract disease 437
            bile duct disease 407
              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

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.