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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:pulmonary tuberculosis
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Accession:DOID:2957 term browser browse the term
Definition:MYCOBACTERIUM infections of the lung.
Synonyms:exact_synonym: Pulmonary Consumption;   Pulmonary Consumptions;   Pulmonary Phthises;   Pulmonary Phthisis;   Pulmonary Tuberculoses
 primary_id: MESH:D014397;   RDO:0006578
 xref: ICD10CM:A15;   ICD9CM:011;   NCI:C26899
For additional species annotation, visit the Alliance of Genome Resources.


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pulmonary tuberculosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb1a ATP binding cassette subfamily B member 1A treatment ISO DNA:SNP: :2677G>A (human) RGD PMID:26067842 RGD:11098541 NCBI chr 4:22,339,829...22,517,642
Ensembl chr 4:22,133,521...22,425,515
JBrowse link
G Ada adenosine deaminase ISO protein:increased expression:plasma, respiratory system fluid/secretion RGD PMID:12194640 RGD:5128854 NCBI chr 3:160,115,840...160,139,947
Ensembl chr 3:160,115,842...160,139,947
JBrowse link
G Adipoq adiponectin, C1Q and collagen domain containing ISO protein:increased expression:plasma RGD PMID:22022605 RGD:5686405 NCBI chr11:81,330,845...81,344,488
Ensembl chr11:81,330,293...81,344,488
JBrowse link
G Akt1 AKT serine/threonine kinase 1 susceptibility ISO DNA:SNP,haplotype:intron: IVS3+18 C/C (human) RGD PMID:20141546 RGD:38676498 NCBI chr 6:137,218,398...137,239,970
Ensembl chr 6:137,218,376...137,236,258
JBrowse link
G Alox5 arachidonate 5-lipoxygenase susceptibility ISO DNA:polymorphism, repeat:promoter, exon:g.760G>A (human) RGD PMID:18174194 RGD:4890411 NCBI chr 4:148,398,004...148,446,308
Ensembl chr 4:148,398,892...148,446,303
JBrowse link
G Asap1 ArfGAP with SH3 domain, ankyrin repeat and PH domain 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25774636 NCBI chr 7:104,670,076...104,951,090
Ensembl chr 7:104,669,672...104,801,045
JBrowse link
G Atf3 activating transcription factor 3 ISO mRNA,protein:increased expression:lung RGD PMID:20856677 RGD:34888225 NCBI chr13:109,817,892...109,849,632
Ensembl chr13:109,817,728...109,849,632
JBrowse link
G C3 complement C3 ISO RGD PMID:19472039 RGD:5129500 NCBI chr 9:9,721,137...9,747,084
Ensembl chr 9:9,721,105...9,747,167
JBrowse link
G Ccl1 C-C motif chemokine ligand 1 susceptibility ISO mRNA:increased expression:lung, dendritic cell
DNA:SNP: :multiple (human)
RGD PMID:18703681, PMID:19057661 RGD:4891409, RGD:4891408 NCBI chr10:69,534,976...69,537,836
Ensembl chr10:69,534,933...69,537,882
JBrowse link
G Ccl19 C-C motif chemokine ligand 19 ISO mRNA:increased expression:lung RGD PMID:19933855 RGD:5130906 NCBI chr 5:58,181,025...58,182,969
Ensembl chr 5:58,181,026...58,183,017
JBrowse link
G Ccl2 C-C motif chemokine ligand 2 susceptibility ISO DNA:polymorphism: :-2518A>G (human)
CTD Direct Evidence: marker/mechanism
CTD PMID:16352737 PMID:18940815, PMID:20111728 RGD:4891439 NCBI chr10:69,412,065...69,413,863
Ensembl chr10:69,412,017...69,413,870
JBrowse link
G Ccl5 C-C motif chemokine ligand 5 susceptibility ISO DNA:snps:5' utr:g.-403G>A rs2280788, g.-28C>G rs2107538 (human)
mRNA:increased expression:lung (human)
RGD PMID:19335954, PMID:15128813 RGD:4891879, RGD:4892112 NCBI chr10:70,739,764...70,744,303
Ensembl chr10:70,739,800...70,744,315
JBrowse link
G Ccr2 C-C motif chemokine receptor 2 disease_progression ISO RGD PMID:11438742 RGD:734715
G Ccr5 C-C motif chemokine receptor 5 ISO protein:decreased expression:blood, T cell (human) RGD PMID:16379602 RGD:4892094 NCBI chr 8:133,192,398...133,215,599
Ensembl chr 8:133,197,032...133,215,614
JBrowse link
G Cd14 CD14 molecule susceptibility ISO DNA:polymorphism:promoter:c. -159C>T (human)|protein:increased expression:monocyte, serum RGD PMID:18008256, PMID:18008256 RGD:4144205, RGD:4144205 NCBI chr18:29,560,341...29,562,290
Ensembl chr18:29,560,365...29,562,153
JBrowse link
G Cd209 CD209 molecule susceptibility ISO CTD Direct Evidence: marker/mechanism
associated with HIV Seropositivity; DNA:SNP:promoter: -336A>G (rs4804803) (human)
DNA:SNPs:promoter:-139G>A, -336A>G, -871A>G (rs2287886,rs4804803,rs735239) (human)
CTD PMID:16379498, PMID:19126442, PMID:24874302 RGD:39939062, RGD:39938981 NCBI chr12:2,406,879...2,413,324
Ensembl chr12:2,406,879...2,413,324
JBrowse link
G Cd274 CD274 molecule ISO protein:increased expression:Tcell, B cell, monocyte RGD PMID:23661793 RGD:40818418 NCBI chr 1:247,519,890...247,539,659
Ensembl chr 1:247,519,939...247,537,943
JBrowse link
G Cd86 CD86 molecule ISO protein:decreased expression:sputum, macrophage (human) RGD PMID:17713660 RGD:4892339 NCBI chr11:67,060,305...67,117,990
Ensembl chr11:67,082,193...67,118,795
JBrowse link
G Clec4m C-type lectin domain family 4 member M susceptibility ISO DNA:repeats:exon 4: allele 4, allele 5, allele 9 (human) RGD PMID:19770268, PMID:24874302, PMID:17224292 RGD:39938983, RGD:39938981, RGD:39938987 NCBI chr12:2,817,633...2,826,303
Ensembl chr12:2,816,065...2,826,378
JBrowse link
G Crp C-reactive protein severity ISO associated with HIV Infections RGD PMID:21219690, PMID:21197091 RGD:5131284, RGD:5131287 NCBI chr13:91,080,448...91,081,358
Ensembl chr13:91,054,974...91,093,713
JBrowse link
G Cxcl10 C-X-C motif chemokine ligand 10 treatment ISO RGD PMID:29843631 RGD:27095956 NCBI chr14:17,210,733...17,212,930
Ensembl chr14:17,210,733...17,212,930
JBrowse link
G Cxcl2 C-X-C motif chemokine ligand 2 disease_progression ISO RGD PMID:20454613 RGD:5135037 NCBI chr14:18,731,346...18,733,391
Ensembl chr14:18,731,378...18,733,391
JBrowse link
G Cxcl6 C-X-C motif chemokine ligand 6 susceptibility ISO mRNA:increased expression:lung RGD PMID:16790804 RGD:5135246 NCBI chr14:18,860,201...18,920,839
Ensembl chr14:18,860,264...18,862,407
JBrowse link
G Cyba cytochrome b-245 alpha chain no_association ISO DNA:SNPs:exons:214C>T (rs4673), 521C>T (rs17845095) (human) RGD PMID:16608528 RGD:4780358 NCBI chr19:55,249,634...55,257,824
Ensembl chr19:55,249,616...55,257,876
JBrowse link
G Ddit3 DNA-damage inducible transcript 3 ISO mRNA,protein:increased expression:lung RGD PMID:20856677 RGD:34888225 NCBI chr 7:70,578,564...70,585,074
Ensembl chr 7:70,580,198...70,585,084
JBrowse link
G Egfr epidermal growth factor receptor disease_progression ISO associated with lung adenocarcinoma; RGD PMID:29621876, PMID:22173705 RGD:38599162, RGD:38599176 NCBI chr14:99,919,485...100,104,136
Ensembl chr14:99,919,485...100,098,796
JBrowse link
G Ereg epiregulin susceptibility ISO DNA:SNP:exon 4: (rs2367707) (human) RGD PMID:30634928 RGD:39457687 NCBI chr14:18,577,620...18,591,395
Ensembl chr14:18,576,355...18,591,394
JBrowse link
G Foxp3 forkhead box P3 susceptibility ISO DNA:polymorphism:promoter:-924A>G(human) RGD PMID:29020928 RGD:38501101 NCBI chr  X:15,753,175...15,768,648
Ensembl chr  X:15,753,175...15,768,522
JBrowse link
G Gbe1 1,4-alpha-glucan branching enzyme 1 ISO DNA:SNP:intron:rs2307058 (human) RGD PMID:28355295 RGD:18337291 NCBI chr11:7,210,169...7,485,895
Ensembl chr11:7,210,209...7,485,890
JBrowse link
G Gstm1 glutathione S-transferase mu 1 susceptibility ISO associated with GSTT1 null deletion; DNA:deletion: : RGD PMID:20297661 RGD:4140932 NCBI chr 2:210,803,869...210,809,461
Ensembl chr 2:210,803,869...210,809,306
JBrowse link
G Gstt1 glutathione S-transferase theta 1 susceptibility ISO DNA:deletion: : RGD PMID:20297661 RGD:4140932 NCBI chr20:13,799,102...13,816,527
Ensembl chr20:13,799,102...13,816,526
JBrowse link
G Havcr2 hepatitis A virus cellular receptor 2 ISO RGD PMID:21382414 RGD:5135524 NCBI chr10:31,561,838...31,590,624
Ensembl chr10:31,561,895...31,588,943
JBrowse link
G Ido1 indoleamine 2,3-dioxygenase 1 treatment ISO RGD PMID:32369456 RGD:39939073 NCBI chr16:72,216,326...72,228,098
Ensembl chr16:72,216,326...72,228,098
JBrowse link
G Il13 interleukin 13 ISO mRNA:increased expression:Leukocytes, Mononuclear RGD PMID:10608794 RGD:4145649 NCBI chr10:38,982,909...38,985,466
Ensembl chr10:38,982,909...38,985,466
JBrowse link
G Il15 interleukin 15 ISO mRNA, protein:increased expression:lung RGD PMID:11742275 RGD:4990461 NCBI chr19:23,542,606...23,624,366
Ensembl chr19:23,542,889...23,554,594
JBrowse link
G Il18 interleukin 18 ISO protein:increased expression:serum RGD PMID:15955140 RGD:4889836 NCBI chr 8:55,009,666...55,016,286
Ensembl chr 8:54,993,859...55,016,299
JBrowse link
G Il1a interleukin 1 alpha ISO RGD PMID:9176116 RGD:4142835 NCBI chr 3:121,824,712...121,836,122
Ensembl chr 3:121,825,412...121,836,086
JBrowse link
G Il1b interleukin 1 beta severity
susceptibility
ISO protein:increased expression:lung
DNA:polymorphism: :3953T>C (human)
protein:increased expression:bronchioalveolar lavage fluid (human)
RGD PMID:10543265, PMID:16634865, PMID:10631206 RGD:4143180, RGD:5147843, RGD:4143179 NCBI chr 3:121,876,256...121,882,637
Ensembl chr 3:121,876,263...121,882,726
JBrowse link
G Il1rl1 interleukin 1 receptor-like 1 ISO RGD PMID:28128217 RGD:39938965 NCBI chr 9:47,133,483...47,184,316
Ensembl chr 9:47,134,034...47,182,170
JBrowse link
G Il1rn interleukin 1 receptor antagonist severity ISO protein:increased expression:lung, serum RGD PMID:10543265, PMID:14619382, PMID:10631206 RGD:4143180, RGD:4143174, RGD:4143179 NCBI chr 3:1,449,778...1,468,624
Ensembl chr 3:1,452,644...1,468,614
JBrowse link
G Il23a interleukin 23 subunit alpha ISO mRNA:increased expression:lung (mouse) RGD PMID:16002675, PMID:21156751, PMID:20624887, PMID:11801672 RGD:39457949, RGD:39458038, RGD:39458036, RGD:39457953 NCBI chr 7:2,710,609...2,712,723
Ensembl chr 7:2,710,609...2,712,723
JBrowse link
G Il27ra interleukin 27 receptor subunit alpha ISO RGD PMID:15749890 RGD:5128486 NCBI chr19:25,151,835...25,163,995
Ensembl chr19:25,149,897...25,164,086
JBrowse link
G Il33 interleukin 33 ISO RGD PMID:28128217 RGD:39938965 NCBI chr 1:248,112,611...248,147,030
Ensembl chr 1:248,132,090...248,147,029
JBrowse link
G Il4 interleukin 4 severity ISO RGD PMID:20832364 RGD:5128550 NCBI chr10:38,963,979...38,969,531
Ensembl chr10:38,963,979...38,969,531
JBrowse link
G Il4r interleukin 4 receptor ISO protein:decreased expression:serum RGD PMID:21251883 RGD:5128510 NCBI chr 1:196,942,343...196,967,221
Ensembl chr 1:196,942,364...196,967,220
JBrowse link
G Il6 interleukin 6 ISO RGD PMID:20624776 RGD:4143257 NCBI chr 4:3,043,231...3,047,807
Ensembl chr 4:3,043,231...3,047,807
JBrowse link
G Il6r interleukin 6 receptor ISO protein:decreased expression:T cell RGD PMID:20019339 RGD:5128632 NCBI chr 2:189,196,180...189,255,987
Ensembl chr 2:189,205,701...189,254,628
JBrowse link
G Irf1 interferon regulatory factor 1 ISO RGD PMID:11083808 RGD:5128719 NCBI chr10:39,109,530...39,116,532
Ensembl chr10:39,109,522...39,116,531
JBrowse link
G Itih4 inter-alpha-trypsin inhibitor heavy chain 4 ISO protein:increased expression:urine RGD PMID:29636444 RGD:40903003 NCBI chr16:6,970,367...6,985,538
Ensembl chr16:6,970,342...6,985,579
JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISO protein:decreased phosphorylation:macrophage, nucleus RGD PMID:19737230 RGD:4889999 NCBI chr 5:114,011,184...114,014,277
Ensembl chr 5:114,011,189...114,014,277
JBrowse link
G Lta lymphotoxin alpha susceptibility ISO DNA:polymorphism:intron:252G>A (human) RGD PMID:20180006 RGD:4143234 NCBI chr20:4,851,889...4,854,677
Ensembl chr20:4,852,496...4,854,677
JBrowse link
G Mbl2 mannose binding lectin 2 ISO DNA:polymorphisms:5' utr, exon:multiple (human) RGD PMID:19199550 RGD:4889452 NCBI chr 1:248,435,069...248,442,669
Ensembl chr 1:248,723,397...248,729,962
JBrowse link
G Mif macrophage migration inhibitory factor susceptibility ISO DNA:SNP: :rs755622 (human) RGD PMID:20439102 RGD:4891004 NCBI chr20:13,715,219...13,732,980
Ensembl chr20:13,732,198...13,732,859
JBrowse link
G Mir30a microRNA 30a disease_progression ISO RGD PMID:25866116 RGD:35668864 NCBI chr 9:29,542,635...29,542,705
Ensembl chr 9:29,542,635...29,542,705
JBrowse link
G Mmp3 matrix metallopeptidase 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24890593 NCBI chr 8:5,676,608...5,698,579
Ensembl chr 8:5,676,665...5,698,579
JBrowse link
G Mmp7 matrix metallopeptidase 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24890593 NCBI chr 8:5,893,253...5,900,965
Ensembl chr 8:5,893,249...5,901,049
JBrowse link
G Mmp8 matrix metallopeptidase 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24890593 NCBI chr 8:5,768,808...5,777,741
Ensembl chr 8:5,768,811...5,778,702
JBrowse link
G Mmp9 matrix metallopeptidase 9 ISO RGD PMID:16982845 RGD:5130746 NCBI chr 3:161,413,410...161,421,473
Ensembl chr 3:161,413,298...161,421,520
JBrowse link
G Nat2 N-acetyltransferase 2 susceptibility ISO RGD PMID:20297661 RGD:4140932 NCBI chr16:23,960,709...23,991,570
Ensembl chr16:23,961,067...23,991,570
JBrowse link
G Nod2 nucleotide-binding oligomerization domain containing 2 susceptibility ISO DNA:SNPs:CDs:p.P268S, R702W, A725G (human) RGD PMID:18419343 RGD:5131510 NCBI chr19:19,342,061...19,389,366
Ensembl chr19:19,332,594...19,377,492
JBrowse link
G Nos2 nitric oxide synthase 2 ISO DNA:SNPs:multiple (human) RGD PMID:19575238 RGD:4144122 NCBI chr10:66,188,290...66,221,621
Ensembl chr10:66,189,786...66,313,190
JBrowse link
G Pdcd1 programmed cell death 1 treatment ISO protein:increased expression:Tcell, B cell, monocyte RGD PMID:23661793, PMID:23661793 RGD:40818418, RGD:40818418 NCBI chr 9:101,305,742...101,319,937
Ensembl chr 9:101,307,764...101,319,845
JBrowse link
G Pdcd1lg2 programmed cell death 1 ligand 2 ISO protein:increased expression:Tcell, B cell, monocyte RGD PMID:23661793 RGD:40818418 NCBI chr 1:247,562,202...247,629,279
Ensembl chr 1:247,562,202...247,627,193
JBrowse link
G Plaur plasminogen activator, urokinase receptor severity ISO RGD PMID:18359089 RGD:6483832 NCBI chr 1:81,328,171...81,344,954
Ensembl chr 1:81,328,183...81,344,708
JBrowse link
G Ptpn22 protein tyrosine phosphatase, non-receptor type 22 ISO DNA:SNPs:cds:788G>A, 1858C>T (human) RGD PMID:19563523 RGD:6484723 NCBI chr 2:206,342,066...206,390,348
Ensembl chr 2:206,342,066...206,390,348
JBrowse link
G RT1-Bb RT1 class II, locus Bb disease_progression
susceptibility
ISO DNA:polymorphisms (human)
DNA:polymorphism: :HLA-DQB1*3:03(human)
DNA:polymorphism:cds:HLA-DQB1*0201(human)
RGD PMID:19230186, PMID:28612994, PMID:24024195 RGD:5147614, RGD:36049765, RGD:36049753 NCBI chr20:4,043,726...4,049,367
Ensembl chr20:4,039,413...4,049,711
JBrowse link
G RT1-Db1 RT1 class II, locus Db1 susceptibility ISO DNA:polymorphism:cds:HLA-DRB1*0201(human)
DNA:polymorphism: :HLA-DRB1*09:01(human)
RGD PMID:24024195, PMID:28612994 RGD:36049753, RGD:36049765 NCBI chr20:4,087,621...4,097,190
Ensembl chr20:4,087,618...4,097,190
JBrowse link
G Sftpa1 surfactant protein A1 susceptibility ISO DNA:SNPs:exons:307G>A, 776C>T (human)
DNA:SNP:intron:1416C>T (human)
RGD PMID:16292672, PMID:12476938 RGD:4144874, RGD:4144875 NCBI chr16:18,716,019...18,719,404
Ensembl chr16:18,716,019...18,719,403
JBrowse link
G Slc11a1 solute carrier family 11 member 1 susceptibility ISO DNA:polymorphism:intron (human)
DNA:deletion:3'UTR:
RGD PMID:21169917, PMID:24024195 RGD:5684974, RGD:36049753 NCBI chr 9:81,655,590...81,666,697
Ensembl chr 9:81,655,629...81,666,706
JBrowse link
G Tap1 transporter 1, ATP binding cassette subfamily B member ISO associated with HIV Infections; RGD PMID:21843574 RGD:6482248 NCBI chr20:3,979,302...3,989,669
Ensembl chr20:3,979,035...3,989,669
JBrowse link
G Tap2 transporter 2, ATP binding cassette subfamily B member susceptibility ISO DNA:polymorphism: : RGD PMID:9062973 RGD:5147851 NCBI chr20:3,995,544...4,009,587
Ensembl chr20:3,995,544...4,009,587
JBrowse link
G Tlr1 toll-like receptor 1 ISO mRNA:increased expression:blood RGD PMID:16493059 RGD:4889525 NCBI chr14:45,062,662...45,065,014
Ensembl chr14:45,062,662...45,081,991
JBrowse link
G Tlr2 toll-like receptor 2 susceptibility ISO DNA:polymorphism:intron (human)
mRNA, protein:increased expression:blood, T cell
DNA:SNP: :rs1816702 (human)
DNA:polymorphisms: :multiple (human)
RGD PMID:20298136, PMID:19552525, PMID:19723394, PMID:20113509 RGD:4145304, RGD:4145355, RGD:4145323, RGD:4145320 NCBI chr 2:182,840,171...182,846,061
Ensembl chr 2:182,840,727...182,846,061
JBrowse link
G Tlr4 toll-like receptor 4 severity
susceptibility
ISO DNA:polymorphisms:cds: p. D299F, T399I (human)
DNA:SNP:intron: rs5030729 (human)
protein:increased expression:monocyte
RGD PMID:20403143, PMID:19575238, PMID:18008256 RGD:4144106, RGD:4144122, RGD:4144205 NCBI chr 5:82,587,424...82,601,056
Ensembl chr 5:82,587,420...82,601,052
JBrowse link
G Tlr9 toll-like receptor 9 ISO DNA:snps:multiple (human) RGD PMID:19771452 RGD:5130704 NCBI chr 8:114,916,122...114,920,171
Ensembl chr 8:114,916,122...114,920,171
JBrowse link
G Tnf tumor necrosis factor susceptibility
disease_progression
ISO DNA:polymorphisms::c.-857 C>T, c. -863 A>C (human) RGD PMID:20650298, PMID:9176116, PMID:18212516 RGD:4143388, RGD:4142835, RGD:4143395 NCBI chr20:5,189,382...5,192,000
Ensembl chr20:5,189,390...5,192,000
JBrowse link
G Vdr vitamin D receptor susceptibility ISO DNA:SNP (human)
DNA:SNPs (human)
DNA:SNPs:promoter, 3' UTR (human)
DNA:SNPs:5' UTR (human)
RGD PMID:17236578, PMID:15295697, PMID:18231846, PMID:18397302, PMID:20231985 RGD:4889849, RGD:4889853, RGD:4889845, RGD:4889842, RGD:4889830 NCBI chr 7:139,344,452...139,394,138
Ensembl chr 7:139,342,063...139,394,166
JBrowse link
Silicotuberculosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Sting1 stimulator of interferon response cGAMP interactor 1 severity ISO RGD PMID:31141689 RGD:39128194 NCBI chr18:28,529,537...28,535,828
Ensembl chr18:28,529,576...28,535,828
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16091
    disease of anatomical entity 15341
      respiratory system disease 2711
        lung disease 1600
          pulmonary tuberculosis 78
            Silicotuberculosis 1
Path 2
Term Annotations click to browse term
  disease 16091
    disease by infectious agent 1808
      Bacterial Infections and Mycoses 695
        bacterial infectious disease 586
          Gram-Positive Bacterial Infections 202
            Actinomycetales Infections 149
              Mycobacterium Infections 148
                tuberculosis 111
                  pulmonary tuberculosis 78
                    Silicotuberculosis 1
paths to the root