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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:extrapulmonary tuberculosis
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Accession:DOID:0050598 term browser browse the term
Definition:A tuberculosis that occurs at body sites other than the lung. (DO)
Synonyms:primary_id: MESH:D000092225


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extrapulmonary tuberculosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cd209d CD209d molecule susceptibility ISO DNA:SNPs:promoter: -939G>A,-871A>G (rs735239) (human) RGD PMID:24874302 RGD:39938981 NCBI chr12:1,891,109...1,897,559
Ensembl chr12:1,891,113...1,901,171 		JBrowse link
G Clec4m C-type lectin domain family 4 member M susceptibility ISO DNA:repeats:exon 4: allele 6, allele 9 (human) RGD PMID:24874302 RGD:39938981 NCBI chr12:1,915,902...1,924,529
Ensembl chr12:1,915,919...1,924,539 		JBrowse link
G Ereg epiregulin susceptibility ISO DNA:SNP:exon 4: (rs2367707) (human) RGD PMID:30634928 RGD:39457687 NCBI chr14:17,027,287...17,041,062
Ensembl chr14:17,027,287...17,041,062 		JBrowse link
Meningeal Tuberculosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Il4r interleukin 4 receptor ISO protein:decreased expression:serum RGD PMID:21251883 RGD:5128510 NCBI chr 1:180,115,061...180,139,981
Ensembl chr 1:180,115,120...180,139,980 		JBrowse link
G Tnf tumor necrosis factor ISO RGD PMID:10318940 RGD:10449456 NCBI chr20:3,622,011...3,624,629
Ensembl chr20:3,622,011...3,624,629 		JBrowse link
pleural tuberculosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ada adenosine deaminase ISO protein:increased activity:pleural fluid:
protein:increased activity:serum:
protein:increased expression:serum:		 RGD PMID:21860532 PMID:1818842 PMID:1689629 PMID:18357489 RGD:152995280, RGD:152998934, RGD:152995292, RGD:152995288 NCBI chr 3:152,398,745...152,422,854
Ensembl chr 3:152,398,747...152,447,088 		JBrowse link
G Ccl22 C-C motif chemokine ligand 22 ISO RGD PMID:20337996 RGD:4891473 NCBI chr19:10,257,602...10,264,373
Ensembl chr19:10,257,601...10,264,400 		JBrowse link
G Ccr2 C-C motif chemokine receptor 2 ISO RGD PMID:19159432 RGD:4145106 NCBI chr 8:123,734,465...123,742,483
Ensembl chr 8:123,734,430...123,742,100 		JBrowse link
G Ccr5 C-C motif chemokine receptor 5 ISO protein:increased expression:pleural fluid, natural killer cell (human) RGD PMID:19159432 RGD:4145106 NCBI chr 8:123,752,423...123,757,538
Ensembl chr 8:123,752,325...123,759,260 		JBrowse link
G Foxp3 forkhead box P3 disease_progression ISO associated with human immunodeficiency virus infectious disease; RGD PMID:21303360 RGD:36947878 NCBI chr  X:14,908,494...14,924,994
Ensembl chr  X:14,908,494...14,923,838 		JBrowse link
G Il1b interleukin 1 beta ISO DNA:polymorphism: :3953T>C (human) RGD PMID:10377182 RGD:4143226 NCBI chr 3:116,577,005...116,583,386
Ensembl chr 3:116,577,010...116,583,415 		JBrowse link
G Il1rn interleukin 1 receptor antagonist ISO DNA:repeat (human) RGD PMID:10377182 RGD:4143226 NCBI chr 3:7,111,567...7,127,451
Ensembl chr 3:7,111,550...7,127,445 		JBrowse link
G Il27 interleukin 27 exacerbates ISO associated with Pleural Effusion;protein:increased expression:pleural fluid (human)
protein:increased expression:alveolar system (human)		 RGD PMID:25753767 PMID:31819557 PMID:23962500 PMID:28844060 RGD:126790505, RGD:126790549, RGD:126790523, RGD:126790517 NCBI chr 1:181,173,108...181,178,720
Ensembl chr 1:181,173,372...181,178,582 		JBrowse link
G Il33 interleukin 33 ISO protein:increased expression:pleural fluid: RGD PMID:23301222 RGD:39939042 NCBI chr 1:227,701,964...227,736,374
Ensembl chr 1:227,721,435...227,736,373 		JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO protein:increased expression:pleura: RGD PMID:18715875 RGD:5129700 NCBI chr 3:153,684,158...153,692,118
Ensembl chr 3:153,683,858...153,692,120 		JBrowse link
G Tlr4 toll-like receptor 4 ISO RGD PMID:18295348 RGD:4144193 NCBI chr 5:80,145,867...80,159,501
Ensembl chr 5:80,145,826...80,159,628 		JBrowse link
G Tnc tenascin C ISO protein:increased expression:pleura RGD PMID:10950882 RGD:4889594 NCBI chr 5:77,375,851...77,460,712
Ensembl chr 5:77,375,851...77,460,624 		JBrowse link
renal tuberculosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Il4r interleukin 4 receptor ISO protein:decreased expression:serum
DNA:polymorphism:cds:p.I50V (human)		 RGD PMID:21251883 PMID:19548368 RGD:5128510, RGD:7207069 NCBI chr 1:180,115,061...180,139,981
Ensembl chr 1:180,115,120...180,139,980 		JBrowse link
Spinal Tuberculoses term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G RT1-Ba RT1 class II, locus Ba susceptibility ISO DNA:missense mutation:CDS:c.592C>G (p.Q198E) (human) RGD PMID:29795056 RGD:126928140 NCBI chr20:4,575,134...4,579,727
Ensembl chr20:4,575,134...4,579,744 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18969
    disease by infectious agent 2215
      Bacterial Infections and Mycoses 1073
        bacterial infectious disease 824
          primary bacterial infectious disease 197
            tuberculosis 130
              extrapulmonary tuberculosis 18
                Cutaneous Tuberculosis + 0
                abdominal tuberculosis + 0
                central nervous system tuberculosis + 2
                lymph node tuberculosis + 0
                miliary tuberculosis 0
                pericardial tuberculosis 0
                pleural tuberculosis + 12
                skeletal tuberculosis + 1
                urogenital tuberculosis + 1
Path 2
Term Annotations click to browse term
  disease 18969
    disease by infectious agent 2215
      Bacterial Infections and Mycoses 1073
        bacterial infectious disease 824
          Gram-Positive Bacterial Infections 395
            Actinomycetales Infections 320
              Mycobacterium Infections 319
                tuberculosis 130
                  extrapulmonary tuberculosis 18
                    Cutaneous Tuberculosis + 0
                    abdominal tuberculosis + 0
                    central nervous system tuberculosis + 2
                    lymph node tuberculosis + 0
                    miliary tuberculosis 0
                    pericardial tuberculosis 0
                    pleural tuberculosis + 12
                    skeletal tuberculosis + 1
                    urogenital tuberculosis + 1
paths to the root