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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:commensal bacterial infectious disease
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Accession:DOID:0050339 term browser browse the term
Definition:A bacterial infectious disease that results_in infection by bacteria which are part of the normal human flora when one or more of the defense mechanisms designed to restrict them from the usually sterile internal tissues are breached by accident, by intent (surgery), or by an underlying metabolic or an infectious disorder. (DO)
Synonyms:primary_id: RDO:9002545


show annotations for term's descendants           Sort by:
chlamydia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ccr5 C-C motif chemokine receptor 5 ISO RGD PMID:16118671 RGD:8549760 NCBI chr 8:123,752,423...123,757,538
Ensembl chr 8:123,752,325...123,759,260 		JBrowse link
G Cd40 CD40 molecule ISO RGD PMID:20102413 RGD:5132268 NCBI chr 3:153,790,372...153,805,279
Ensembl chr 3:153,790,449...153,805,534 		JBrowse link
G Foxp3 forkhead box P3 treatment ISO RGD PMID:30832593 RGD:38455984 NCBI chr  X:14,908,494...14,924,994
Ensembl chr  X:14,908,494...14,923,838 		JBrowse link
G Icam1 intercellular adhesion molecule 1 ISO mRNA:increased expression:lung (mouse) RGD PMID:19728926 RGD:4145507 NCBI chr 8:19,553,063...19,565,438
Ensembl chr 8:19,553,645...19,565,438 		JBrowse link
G Ido1 indoleamine 2,3-dioxygenase 1 treatment ISO mRNA:increased expression:lung (mouse) RGD PMID:30832593 PMID:31249813 RGD:38455984, RGD:39938856 NCBI chr16:67,430,654...67,442,726
Ensembl chr16:67,430,578...67,442,730 		JBrowse link
G Ifng interferon gamma ISO CTD Direct Evidence: marker/mechanism CTD PMID:19203382 NCBI chr 7:53,903,339...53,907,375
Ensembl chr 7:53,903,337...53,907,375 		JBrowse link
G Il13 interleukin 13 ISO RGD PMID:21573182 RGD:5684365 NCBI chr10:37,790,130...37,792,687
Ensembl chr10:37,790,130...37,792,737 		JBrowse link
G Il17a interleukin 17A ISO associated with Bronchial Hyprractivity; mRNA:increased expression:lung RGD PMID:20228193 PMID:19812198 RGD:4888528, RGD:4889101 NCBI chr 9:23,144,402...23,147,889
Ensembl chr 9:23,144,402...23,147,889 		JBrowse link
G Mir21 microRNA 21 ISO associated with asthma;RNA:increased expression:lung RGD PMID:27448447 RGD:41404696 NCBI chr10:71,405,257...71,405,348
Ensembl chr10:71,405,257...71,405,348 		JBrowse link
G Tgfb1 transforming growth factor, beta 1 treatment ISO RGD PMID:30832593 RGD:38455984 NCBI chr 1:81,196,532...81,212,848
Ensembl chr 1:81,196,532...81,212,847 		JBrowse link
G Tnf tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:19203382 NCBI chr20:3,622,011...3,624,629
Ensembl chr20:3,622,011...3,624,629 		JBrowse link
Chlamydia pneumonia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cd274 CD274 molecule ISO mRNA:increased expression:lung RGD PMID:26378990 RGD:41412180 NCBI chr 1:227,116,674...227,137,379
Ensembl chr 1:227,116,649...227,134,450 		JBrowse link
G Pdcd1 programmed cell death 1 ISO mRNA:increased expression:lung RGD PMID:26378990 RGD:41412180 NCBI chr 9:94,418,786...94,431,945
Ensembl chr 9:94,418,791...94,431,937 		JBrowse link
G Pik3cd phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta severity ISO RGD PMID:29893841 RGD:40890270 NCBI chr 5:160,094,952...160,142,962
Ensembl chr 5:160,094,952...160,120,930 		JBrowse link
gas gangrene term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Gsn gelsolin ISO protein:decreased expression:blood serum (human) RGD PMID:9142022 RGD:329333022 NCBI chr 3:18,585,166...18,638,404
Ensembl chr 3:18,585,172...18,638,402 		JBrowse link
toxic shock syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G A2m alpha-2-macroglobulin treatment IDA RGD PMID:2424486 RGD:10046036 NCBI chr 4:154,897,770...154,947,787
Ensembl chr 4:154,897,877...154,947,786 		JBrowse link
G Ace angiotensin I converting enzyme severity ISO DNA:SNP, insertion/deletion:promoter, intron: (rs4291, rs4646994) RGD PMID:28336767 RGD:39939121 NCBI chr10:90,910,316...90,930,437
Ensembl chr10:90,910,316...90,931,131 		JBrowse link
G Adk adenosine kinase ISO RGD PMID:8207212 RGD:6482670 NCBI chr15:2,863,241...3,246,453
Ensembl chr15:2,863,244...3,246,510 		JBrowse link
G Adm adrenomedullin IDA
IMP		 RGD PMID:17318497 PMID:17766482 RGD:1625310, RGD:1642599 NCBI chr 1:164,745,484...164,747,655
Ensembl chr 1:164,745,466...164,747,654 		JBrowse link
G Adrb2 adrenoceptor beta 2 disease_progression
treatment		 ISO DNA:polymorphism: :rs1042717(human) RGD PMID:19850944 PMID:16076286 RGD:8548487, RGD:8548529 NCBI chr18:55,642,459...55,644,501
Ensembl chr18:55,502,903...55,644,512 		JBrowse link
G Ager advanced glycosylation end product-specific receptor ISO RGD PMID:21270403 RGD:6767566 NCBI chr20:4,148,150...4,151,361
Ensembl chr20:4,147,890...4,151,078 		JBrowse link
G Aqp1 aquaporin 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24028651 NCBI chr 4:84,482,512...84,494,690
Ensembl chr 4:84,482,512...84,494,690 		JBrowse link
G C5ar1 complement C5a receptor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18063050 NCBI chr 1:76,948,622...76,959,826 JBrowse link
G Cckbr cholecystokinin B receptor IEP mRNA:increased expression:myocardium RGD PMID:15948246 RGD:2311332 NCBI chr 1:159,771,733...159,781,738
Ensembl chr 1:159,771,733...159,814,881 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 disease_progression ISO RGD PMID:28834779 RGD:14995949 NCBI chr10:67,005,424...67,007,222
Ensembl chr10:67,005,424...67,007,226 		JBrowse link
G Cd274 CD274 molecule severity ISO protein:increased expression:serum
protein:increased expression:lymphocyte, mononcyte		 RGD PMID:29702526 PMID:26063974 RGD:40822808, RGD:41410786 NCBI chr 1:227,116,674...227,137,379
Ensembl chr 1:227,116,649...227,134,450 		JBrowse link
G Elane elastase, neutrophil expressed treatment IMP RGD PMID:18323746 RGD:10450579 NCBI chr 7:9,817,251...9,819,174
Ensembl chr 7:9,817,252...9,819,100 		JBrowse link
G Eno2 enolase 2 IEP proteiin:increased expression:serum RGD PMID:17083782 RGD:2293748 NCBI chr 4:157,572,085...157,580,971
Ensembl chr 4:157,572,088...157,580,980 		JBrowse link
G F2 coagulation factor II, thrombin severity ISO protein:decreased expression:blood plasma (human) RGD PMID:2788582 RGD:40822807 NCBI chr 3:77,596,196...77,609,486
Ensembl chr 3:77,596,198...77,609,486 		JBrowse link
G Fancc FA complementation group C ISO RGD PMID:17404312 RGD:11045879 NCBI chr17:1,680,660...1,822,610
Ensembl chr17:1,681,324...1,829,376 		JBrowse link
G Gc GC, vitamin D binding protein ISO CTD Direct Evidence: marker/mechanism CTD PMID:17852808 NCBI chr14:18,632,146...18,667,563
Ensembl chr14:18,632,135...18,667,567 		JBrowse link
G Grk2 G protein-coupled receptor kinase 2 ISO mRNA:decreased expression:polymorphonuclear leukocyte RGD PMID:24465168 RGD:126848796 NCBI chr 1:201,580,823...201,601,580
Ensembl chr 1:201,581,480...201,601,582 		JBrowse link
G Hmox1 heme oxygenase 1 IDA RGD PMID:18208666 RGD:4145362 NCBI chr19:13,466,287...13,474,082
Ensembl chr19:13,467,244...13,474,079 		JBrowse link
G Hspa1b heat shock protein family A (Hsp70) member 1B susceptibility ISO associated wit community-acquired pneumonia;DNA:SNP: :1267A>G (human) RGD PMID:12771604 RGD:5147601 NCBI chr20:3,855,104...3,859,148
Ensembl chr20:3,856,006...3,873,240
Ensembl chr20:3,856,006...3,873,240 		JBrowse link
G Ido1 indoleamine 2,3-dioxygenase 1 severity ISO protein:increased activity, increased expression:plasma, heart (human) RGD PMID:21765346 RGD:39939075 NCBI chr16:67,430,654...67,442,726
Ensembl chr16:67,430,578...67,442,730 		JBrowse link
G Ifng interferon gamma ISO protein:increased expression:plasma RGD PMID:25403265 RGD:38455982 NCBI chr 7:53,903,339...53,907,375
Ensembl chr 7:53,903,337...53,907,375 		JBrowse link
G Il10 interleukin 10 onset
severity		 ISO protein:increased expression:plasma
protein:increased expression:lung (mouse)		 RGD PMID:12117955 PMID:12117955 PMID:7593621 PMID:25403265 PMID:28659355 RGD:1598471, RGD:1598471, RGD:11049456, RGD:38455982, RGD:40890272 NCBI chr13:42,472,625...42,477,308
Ensembl chr13:42,472,839...42,477,313 		JBrowse link
G Il19 interleukin 19 ISO RGD PMID:18246602 RGD:5037232 NCBI chr13:42,397,715...42,411,637
Ensembl chr13:42,399,138...42,405,473 		JBrowse link
G Il1b interleukin 1 beta severity ISO protein:increased expression:lung (mouse) RGD PMID:28659355 RGD:40890272 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 treatment
susceptibility		 ISO human gene in a mouse model
associated with Precursor Cell Lymphoblastic Leukemia-Lymphoma;DNA:polymorphism::		 RGD PMID:15516267 PMID:23014359 RGD:8551736, RGD:11522756 NCBI chr 3:7,111,567...7,127,451
Ensembl chr 3:7,111,550...7,127,445 		JBrowse link
G Il20ra interleukin 20 receptor subunit alpha ISO mRNA:increased expression:multiple RGD PMID:18246602 RGD:5037232 NCBI chr 1:14,424,215...14,494,226
Ensembl chr 1:14,451,228...14,493,602 		JBrowse link
G Il20rb interleukin 20 receptor subunit beta ISO mRNA:increased expression:multiple RGD PMID:18246602 RGD:5037232 NCBI chr 8:100,979,085...101,010,829
Ensembl chr 8:100,980,383...101,009,942 		JBrowse link
G Il27 interleukin 27 ISO protein, mRNA:increased expression:blood serum, spleen (mouse) RGD PMID:20435892 RGD:126790535 NCBI chr 1:181,173,108...181,178,720
Ensembl chr 1:181,173,372...181,178,582 		JBrowse link
G Il6 interleukin 6 treatment ISO RGD PMID:2124237 RGD:11060276 NCBI chr 4:5,214,602...5,219,178
Ensembl chr 4:5,213,394...5,219,178 		JBrowse link
G Mbl2 mannose binding lectin 2 susceptibility ISO associated with acute pyelonephritis;DNA:SNPs, missense mutations, haplotypes:promoter, cds:multiple RGD PMID:17202308 PMID:17202308 RGD:6903268, RGD:6903268 NCBI chr 1:228,016,439...228,024,736 JBrowse link
G Mc2r melanocortin 2 receptor IEP protein:increased expression:liver (rat) RGD PMID:2822467 RGD:6484558 NCBI chr18:62,001,980...62,015,567
Ensembl chr18:62,004,948...62,015,488 		JBrowse link
G Mif macrophage migration inhibitory factor IMP
IDA		 RGD PMID:17381395 PMID:17565848 RGD:4891013, RGD:1641978 NCBI chr20:12,790,919...12,791,784
Ensembl chr20:12,790,902...12,799,504 		JBrowse link
G Mir155 microRNA 155 ISO RGD PMID:29979224 RGD:21081538 NCBI chr11:23,774,654...23,774,718
Ensembl chr11:23,774,654...23,774,718 		JBrowse link
G Mir21 microRNA 21 exacerbates
ameliorates		 ISO RGD PMID:28437377 PMID:31189875 RGD:41404641, RGD:41404698 NCBI chr10:71,405,257...71,405,348
Ensembl chr10:71,405,257...71,405,348 		JBrowse link
G Mir494 microRNA 494 severity ISO RGD PMID:30783439 RGD:150527846 NCBI chr 6:128,728,710...128,728,792
Ensembl chr 6:128,728,709...128,728,793 		JBrowse link
G Mt-nd1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 susceptibility ISO associated with Burns; DNA:missense mutation:cds:m.4216T>C (human) RGD PMID:19487983 RGD:5148017 NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
NCBI chr MT:2,740...3,694
Ensembl chr MT:2,740...3,694 		JBrowse link
G Nfkbia NFKB inhibitor alpha treatment IEP RGD PMID:11961112 RGD:126928137 NCBI chr 6:72,858,713...72,861,941
Ensembl chr 6:72,858,712...72,861,941 		JBrowse link
G Nos2 nitric oxide synthase 2 IDA
ISO		 CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:8745224 PMID:16601845 RGD:1580268 NCBI chr10:63,815,308...63,851,208
Ensembl chr10:63,815,308...63,851,210 		JBrowse link
G Nppc natriuretic peptide C ISO protein:increased expression:plasma RGD PMID:8117275 RGD:1642297 NCBI chr 9:87,320,051...87,324,251
Ensembl chr 9:87,320,051...87,324,251 		JBrowse link
G Ogg1 8-oxoguanine DNA glycosylase ISO RGD PMID:15677345 RGD:8657146 NCBI chr 4:146,474,701...146,481,959
Ensembl chr 4:146,474,750...146,484,766 		JBrowse link
G Parp1 poly (ADP-ribose) polymerase 1 ISO RGD PMID:12445868 RGD:10414070 NCBI chr13:92,307,593...92,339,406
Ensembl chr13:92,307,586...92,339,404 		JBrowse link
G Pdcd1 programmed cell death 1 severity ISO protein:increased expression:serum
protein:increased expression:lymphocyte, mononcyte		 RGD PMID:29702526 PMID:26063974 RGD:40822808, RGD:41410786 NCBI chr 9:94,418,786...94,431,945
Ensembl chr 9:94,418,791...94,431,937 		JBrowse link
G Pik3cd phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta severity ISO RGD PMID:28659355 RGD:40890272 NCBI chr 5:160,094,952...160,142,962
Ensembl chr 5:160,094,952...160,120,930 		JBrowse link
G Plaur plasminogen activator, urokinase receptor ISO RGD PMID:20693875 RGD:6484122 NCBI chr 1:80,053,440...80,068,384
Ensembl chr 1:80,050,324...80,068,595 		JBrowse link
G Proc protein C, inactivator of coagulation factors Va and VIIIa treatment ISO RGD PMID:19320827 PMID:21850534 RGD:11100015, RGD:11100041 NCBI chr18:23,764,367...23,774,816
Ensembl chr18:23,764,368...23,775,133 		JBrowse link
G Ptx3 pentraxin 3 ISO protein:increased expression:plasma (human) RGD PMID:30687307 RGD:38508896 NCBI chr 2:150,487,513...150,493,323
Ensembl chr 2:150,487,513...150,493,323 		JBrowse link
G Ren renin exacerbates ISO protein:increased activity:blood plasma (human) RGD PMID:31723628 RGD:125097502 NCBI chr13:44,796,260...44,807,491
Ensembl chr13:44,796,091...44,807,489 		JBrowse link
G RT1-Da RT1 class II, locus Da disease_progression ISO associated with Burns
CTD Direct Evidence: marker/mechanism		 CTD
RGD		 PMID:28771573 PMID:17568330 PMID:15644645 RGD:5490160, RGD:5490203 NCBI chr20:4,513,464...4,518,457
Ensembl chr20:4,512,911...4,518,455 		JBrowse link
G RT1-Db1 RT1 class II, locus Db1 ISO mRNA:decreased expression:blood RGD PMID:15644645 RGD:5490203 NCBI chr20:4,548,664...4,558,237
Ensembl chr20:4,548,666...4,558,258 		JBrowse link
G Sell selectin L IEP protein:increased expression:plasma RGD PMID:19375498 RGD:5685700 NCBI chr13:76,416,969...76,436,444
Ensembl chr13:76,416,915...76,436,456 		JBrowse link
G Serpinc1 serpin family C member 1 treatment ISO RGD PMID:16732381 RGD:1599323 NCBI chr13:73,257,208...73,271,476
Ensembl chr13:73,257,179...73,284,293 		JBrowse link
G Serpine1 serpin family E member 1 susceptibility ISO associated with Pneumonia; DNA:polymorphism:promoter:rs1799768 (human) RGD PMID:20429897 RGD:4144828 NCBI chr12:19,601,272...19,611,657
Ensembl chr12:19,601,272...19,611,657 		JBrowse link
G Serpinf1 serpin family F member 1 severity ISO protein:decreased expression:plasma (human) RGD PMID:6158114 RGD:36174004 NCBI chr10:60,250,198...60,262,593
Ensembl chr10:60,249,708...60,262,646 		JBrowse link
G Serping1 serpin family G member 1 treatment ISO RGD PMID:8172580 RGD:8661646 NCBI chr 3:69,842,726...69,852,583
Ensembl chr 3:69,842,739...69,852,034 		JBrowse link
G Sftpb surfactant protein B ISO associated with Pneumonia;DNA:polymorphism: :1580C>T (human) RGD PMID:15190959 RGD:4143404 NCBI chr 4:104,359,303...104,368,439
Ensembl chr 4:104,359,396...104,368,436 		JBrowse link
G Socs1 suppressor of cytokine signaling 1 severity ISO RGD PMID:19469017 RGD:150573701 NCBI chr10:4,882,651...4,884,342
Ensembl chr10:4,882,560...4,884,383 		JBrowse link
G Tbxa2r thromboxane A2 receptor treatment IMP RGD PMID:7816742 RGD:11059599 NCBI chr 7:8,383,347...8,390,753
Ensembl chr 7:8,383,378...8,388,176 		JBrowse link
G Tfpi tissue factor pathway inhibitor treatment ISO RGD PMID:11776329 RGD:11062085 NCBI chr 3:69,533,156...69,582,547
Ensembl chr 3:69,533,156...69,576,880 		JBrowse link
G Thpo thrombopoietin ISO protein:increased expression:serum: RGD PMID:20467749 RGD:10449021 Ensembl chr11:80,182,820...80,188,167 JBrowse link
G Tnf tumor necrosis factor treatment IEP
ISO		 CTD Direct Evidence: marker/mechanism
protein:increased expression:peritoneal macrophage, cell surface (rat)		 CTD
RGD		 PMID:20054000 PMID:2213560 PMID:12622907 RGD:10449465, RGD:1598936 NCBI chr20:3,622,011...3,624,629
Ensembl chr20:3,622,011...3,624,629 		JBrowse link
G Trem1 triggering receptor expressed on myeloid cells 1 ISO mRNA:decreased expression:polymorphonuclear leukocyte RGD PMID:24465168 RGD:126848796 NCBI chr 9:12,763,819...12,779,285
Ensembl chr 9:12,763,819...12,779,203 		JBrowse link
G Zc3h12a zinc finger CCCH type containing 12A ISO RGD PMID:23422584 RGD:39938961 NCBI chr 5:137,376,562...137,385,351
Ensembl chr 5:137,376,564...137,385,351 		JBrowse link
trachoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Il10 interleukin 10 no_association
severity		 ISO protein:increased expression:tear
DNA:SNP:promoter:−1082G>A (human)
DNA:SNP:promoter:−819T>C, −592A>C (human)
DNA:SNP, haplotype:promoter:−1082G>A (human)
DNA:haplotype: :		 RGD PMID:18628987 PMID:11023480 PMID:11023480 PMID:15789056 PMID:17947295 RGD:7365037, RGD:7365085, RGD:7365085, RGD:7365072, RGD:7365053 NCBI chr13:42,472,625...42,477,308
Ensembl chr13:42,472,839...42,477,313 		JBrowse link
G Il17a interleukin 17A ISO mRNA:increased expression:conjunctiva (human) RGD PMID:21911461 RGD:9068420 NCBI chr 9:23,144,402...23,147,889
Ensembl chr 9:23,144,402...23,147,889 		JBrowse link
G RT1-CE13 RT1 class I, locus CE13 ISO DNA:polymorphisms:cds:HLA-B*14 (human, Tanzanian) RGD PMID:18824733 RGD:7364877 NCBI chr20:3,314,830...3,318,106 JBrowse link
G Tnf tumor necrosis factor ISO DNA:SNP, haplotypes:promoter:−308G>A (human) RGD PMID:17330135 RGD:8548830 NCBI chr20:3,622,011...3,624,629
Ensembl chr20:3,622,011...3,624,629 		JBrowse link
Trachomatous Trichiasis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Col1a1 collagen type I alpha 1 chain ISO mRNA:decreased expression:tarsal conjunctiva (human) RGD PMID:20375326 RGD:8552676 NCBI chr10:79,883,622...79,900,625
Ensembl chr10:79,883,622...79,900,624 		JBrowse link
Whipple disease term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cd163 CD163 molecule ISO protein:increased expression:duodenum, macrophage (human) RGD PMID:19664628 RGD:149735573 NCBI chr 4:157,085,080...157,118,470
Ensembl chr 4:157,085,093...157,117,878 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19047
    disease by infectious agent 2249
      Bacterial Infections and Mycoses 1115
        bacterial infectious disease 823
          commensal bacterial infectious disease 73
            Lemierre's syndrome 0
            Ritter's disease + 0
            actinobacillosis 0
            actinomycosis + 1
            chlamydia + 17
            gas gangrene 1
            inclusion conjunctivitis 0
            pertussis + 0
            toxic shock syndrome 62
            trachoma + 5
paths to the root