Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)

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
go back to main search page
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

GViewer not supported for the selected species.

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 chr22:7,803,794...7,818,112 JBrowse link
G CD40 CD40 molecule ISO RGD PMID:20102413 RGD:5132268 NCBI chr 2:17,753,713...17,765,134
Ensembl chr 2:17,753,394...17,764,566 		JBrowse link
G FOXP3 forkhead box P3 treatment ISO RGD PMID:30832593 RGD:38455984 NCBI chr  X:46,349,890...46,365,133 JBrowse link
G ICAM1 intercellular adhesion molecule 1 ISO mRNA:increased expression:lung (mouse) RGD PMID:19728926 RGD:4145507 NCBI chr 6:9,320,991...9,338,125
Ensembl chr 6:9,322,550...9,338,263 		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 chr 8:37,930,910...37,950,790
Ensembl chr 8:37,930,562...37,946,505 		JBrowse link
G IFNG interferon gamma ISO CTD Direct Evidence: marker/mechanism CTD PMID:19203382 NCBI chr11:63,785,493...63,791,071
Ensembl chr11:63,786,041...63,790,473 		JBrowse link
G IL13 interleukin 13 ISO RGD PMID:21573182 RGD:5684365 NCBI chr23:35,475,762...35,479,419
Ensembl chr23:35,476,490...35,478,869 		JBrowse link
G IL17A interleukin 17A ISO associated with Bronchial Hyprractivity; mRNA:increased expression:lung RGD PMID:19812198 PMID:20228193 RGD:4888528 RGD:4889101 NCBI chr17:20,314,082...20,319,917
Ensembl chr17:20,315,773...20,318,785 		JBrowse link
G TGFB1 transforming growth factor beta 1 treatment ISO RGD PMID:30832593 RGD:38455984 NCBI chr 6:35,651,583...35,674,387
Ensembl chr 6:35,648,677...35,674,365 		JBrowse link
G TNF tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:19203382
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 chr12:74,038,844...74,060,662
Ensembl chr12:74,041,767...74,056,806 		JBrowse link
G PDCD1 programmed cell death 1 ISO mRNA:increased expression:lung RGD PMID:26378990 RGD:41412180 NCBI chr10:127,877,383...127,886,234
Ensembl chr10:127,878,554...127,886,088 		JBrowse link
G PIK3CD phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta severity ISO RGD PMID:29893841 RGD:40890270 NCBI chr20:122,040,131...122,111,397
Ensembl chr20:122,041,963...122,078,504 		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 chr12:18,253,079...18,317,285
Ensembl chr12:18,253,324...18,285,938 		JBrowse link
toxic shock syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADK adenosine kinase ISO RGD PMID:8207212 RGD:6482670 NCBI chr 9:56,659,284...57,222,279
Ensembl chr 9:56,660,129...57,222,147 		JBrowse link
G ADM adrenomedullin ISO RGD PMID:17318497 PMID:17766482 RGD:1625310 RGD:1642599 NCBI chr 1:54,518,359...54,520,683
Ensembl chr 1:54,518,358...54,520,686 		JBrowse link
G ADRB2 adrenoceptor beta 2 treatment
disease_progression 		ISO DNA:polymorphism: :rs1042717(human) RGD PMID:16076286 PMID:19850944 RGD:8548487 RGD:8548529 NCBI chr23:51,445,920...51,447,942
Ensembl chr23:51,446,154...51,447,401 		JBrowse link
G AGER advanced glycosylation end-product specific receptor ISO RGD PMID:21270403 RGD:6767566 NCBI chr17:39,847,343...39,851,288
Ensembl chr17:39,847,759...39,851,127 		JBrowse link
G AQP1 aquaporin 1 (Colton blood group) ISO CTD Direct Evidence: marker/mechanism CTD PMID:24028651 NCBI chr21:27,456,553...27,473,196
Ensembl chr21:27,456,259...27,470,728 		JBrowse link
G C5AR1 complement C5a receptor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18063050 NCBI chr 6:40,633,540...40,651,839
Ensembl chr 6:40,633,448...40,652,845 		JBrowse link
G CCKBR cholecystokinin B receptor ISO mRNA:increased expression:myocardium RGD PMID:15948246 RGD:2311332 NCBI chr 1:58,555,463...58,569,949
Ensembl chr 1:58,555,321...58,568,031 		JBrowse link
G CCL2 C-C motif chemokine ligand 2 disease_progression ISO RGD PMID:28834779 RGD:14995949 NCBI chr16:27,763,354...27,765,437
Ensembl chr16:27,763,555...27,765,416 		JBrowse link
G CD274 CD274 molecule severity ISO protein:increased expression:serum
protein:increased expression:lymphocyte, mononcyte 		RGD PMID:26063974 PMID:29702526 RGD:40822808 RGD:41410786 NCBI chr12:74,038,844...74,060,662
Ensembl chr12:74,041,767...74,056,806 		JBrowse link
G ELANE elastase, neutrophil expressed treatment ISO RGD PMID:18323746 RGD:10450579 NCBI chr 6:599,392...604,925
Ensembl chr 6:601,217...604,725 		JBrowse link
G ENO2 enolase 2 ISO proteiin:increased expression:serum RGD PMID:17083782 RGD:2293748 NCBI chr11:6,945,243...6,954,959
Ensembl chr11:6,945,413...6,957,304 		JBrowse link
G FANCC FA complementation group C ISO RGD PMID:17404312 RGD:11045879 NCBI chr12:107,780,087...107,991,828
Ensembl chr12:107,845,135...107,991,237 		JBrowse link
G GC GC vitamin D binding protein ISO CTD Direct Evidence: marker/mechanism CTD PMID:17852808 NCBI chr 7:20,254,604...20,298,384
Ensembl chr 7:20,253,879...20,298,265 		JBrowse link
G GRK2 G protein-coupled receptor kinase 2 ISO mRNA:decreased expression:polymorphonuclear leukocyte RGD PMID:24465168 RGD:126848796 NCBI chr 1:6,975,202...6,995,369
Ensembl chr 1:6,975,002...6,995,259 		JBrowse link
G HMOX1 heme oxygenase 1 ISO RGD PMID:18208666 RGD:4145362 NCBI chr19:18,144,466...18,157,944
Ensembl chr19:18,144,545...18,157,971 		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 chr 8:37,930,910...37,950,790
Ensembl chr 8:37,930,562...37,946,505 		JBrowse link
G IFNG interferon gamma ISO protein:increased expression:plasma RGD PMID:25403265 RGD:38455982 NCBI chr11:63,785,493...63,791,071
Ensembl chr11:63,786,041...63,790,473 		JBrowse link
G IL10 interleukin 10 severity
onset 		ISO protein:increased expression:lung (mouse)
protein:increased expression:plasma 		RGD PMID:7593621 PMID:12117955 PMID:25403265 PMID:28659355 RGD:11049456 RGD:1598471 RGD:38455982 RGD:40890272 NCBI chr25:22,590,389...22,595,877
Ensembl chr25:22,590,962...22,594,836 		JBrowse link
G IL19 interleukin 19 ISO protein:increased expression:serum RGD PMID:18246602 RGD:5037232 NCBI chr25:22,514,199...22,523,680
Ensembl chr25:22,514,559...22,520,499 		JBrowse link
G IL1B interleukin 1 beta severity ISO protein:increased expression:lung (mouse) RGD PMID:28659355 RGD:40890272 NCBI chr14:15,844,628...15,852,652
Ensembl chr14:15,844,672...15,850,729 		JBrowse link
G IL1RN interleukin 1 receptor antagonist susceptibility
treatment 		ISO associated with Precursor Cell Lymphoblastic Leukemia-Lymphoma;DNA:polymorphism::
human gene in a mouse model 		RGD PMID:15516267 PMID:23014359 RGD:11522756 RGD:8551736 NCBI chr14:16,136,667...16,152,451
Ensembl chr14:16,146,333...16,151,326 		JBrowse link
G IL20RA interleukin 20 receptor subunit alpha ISO mRNA:increased expression:multiple RGD PMID:18246602 RGD:5037232 NCBI chr13:36,351,873...36,397,300
Ensembl chr13:36,352,018...36,397,302 		JBrowse link
G IL20RB interleukin 20 receptor subunit beta ISO mRNA:increased expression:multiple RGD PMID:18246602 RGD:5037232 NCBI chr15:53,446,410...53,493,827
Ensembl chr15:53,448,034...53,493,618 		JBrowse link
G IL27 interleukin 27 ISO protein, mRNA:increased expression:blood serum, spleen (mouse) RGD PMID:20435892 RGD:126790535 NCBI chr 5:26,348,559...26,358,028
Ensembl chr 5:26,348,848...26,356,360 		JBrowse link
G IL6 interleukin 6 treatment ISO RGD PMID:2124237 RGD:11060276 NCBI chr21:35,577,513...35,582,385
Ensembl chr21:35,577,939...35,582,237 		JBrowse link
G LOC103221743 heat shock 70 kDa protein 1A susceptibility ISO associated wit community-acquired pneumonia;DNA:SNP: :1267A>G (human) RGD PMID:12771604 RGD:5147601 NCBI chr17:40,191,695...40,194,459
Ensembl chr17:40,203,936...40,205,858 		JBrowse link
G LOC103233689 thromboxane A2 receptor treatment ISO RGD PMID:7816742 RGD:11059599 NCBI chr 6:3,354,358...3,365,779
Ensembl chr 6:3,355,314...3,359,761 		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 RGD:6903268 NCBI chr 9:78,389,534...78,394,753
Ensembl chr 9:78,389,947...78,396,079 		JBrowse link
G MC2R melanocortin 2 receptor ISO protein:increased expression:liver (rat) RGD PMID:2822467 RGD:6484558 NCBI chr18:72,286,380...72,296,607
Ensembl chr18:72,288,224...72,289,105 		JBrowse link
G MHC-DRA major histocompatibility complex, class II, DR alpha disease_progression ISO CTD Direct Evidence: marker/mechanism
associated with Burns 		RGD
CTD		 PMID:15644645 PMID:17568330 PMID:28771573 RGD:5490160 RGD:5490203 NCBI chr17:39,623,324...39,628,464
Ensembl chr17:39,622,402...39,629,261 		JBrowse link
G MIF macrophage migration inhibitory factor ISO RGD PMID:17381395 PMID:17565848 RGD:1641978 RGD:4891013 NCBI chr19:7,000,837...7,001,700
Ensembl chr19:7,000,793...7,001,757 		JBrowse link
G NFKBIA NFKB inhibitor alpha treatment ISO RGD PMID:11961112 RGD:126928137 NCBI chr24:12,211,619...12,216,185
Ensembl chr24:12,210,281...12,214,854 		JBrowse link
G NOS2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:8745224 PMID:16601845 RGD:1580268 NCBI chr16:21,533,011...21,576,645
Ensembl chr16:21,533,484...21,574,257 		JBrowse link
G NPPC natriuretic peptide C ISO protein:increased expression:plasma RGD PMID:8117275 RGD:1642297 NCBI chr10:117,919,889...117,924,306
Ensembl chr10:117,919,760...117,924,273 		JBrowse link
G OGG1 8-oxoguanine DNA glycosylase ISO RGD PMID:15677345 RGD:8657146 NCBI chr22:45,757,414...45,763,690 JBrowse link
G PARP1 poly(ADP-ribose) polymerase 1 ISO RGD PMID:12445868 RGD:10414070 NCBI chr25:3,350,798...3,405,040 JBrowse link
G PDCD1 programmed cell death 1 severity ISO protein:increased expression:lymphocyte, mononcyte
protein:increased expression:serum 		RGD PMID:26063974 PMID:29702526 RGD:40822808 RGD:41410786 NCBI chr10:127,877,383...127,886,234
Ensembl chr10:127,878,554...127,886,088 		JBrowse link
G PIK3CD phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta severity ISO RGD PMID:28659355 RGD:40890272 NCBI chr20:122,040,131...122,111,397
Ensembl chr20:122,041,963...122,078,504 		JBrowse link
G PLAUR plasminogen activator, urokinase receptor ISO RGD PMID:20693875 RGD:6484122 NCBI chr 6:37,161,957...37,191,867 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 chr10:2,789,227...2,799,783
Ensembl chr10:2,789,277...2,799,531 		JBrowse link
G PTX3 pentraxin 3 ISO protein:increased expression:plasma (human) RGD PMID:30687307 RGD:38508896 NCBI chr15:33,320,592...33,327,236
Ensembl chr15:33,321,208...33,327,268 		JBrowse link
G REN renin exacerbates ISO protein:increased activity:blood plasma (human) RGD PMID:31723628 RGD:125097502 NCBI chr25:25,159,816...25,193,620
Ensembl chr25:25,183,037...25,193,420 		JBrowse link
G SELL selectin L ISO protein:increased expression:plasma RGD PMID:19375498 RGD:5685700 NCBI chr25:59,345,080...59,365,684
Ensembl chr25:59,345,069...59,366,946 		JBrowse link
G SERPINC1 serpin family C member 1 treatment ISO RGD PMID:16732381 RGD:1599323 NCBI chr25:55,271,823...55,289,855 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 chr28:12,047,520...12,060,662
Ensembl chr28:12,047,529...12,060,202 		JBrowse link
G SERPINF1 serpin family F member 1 severity ISO protein:decreased expression:plasma (human) RGD PMID:6158114 RGD:36174004 NCBI chr16:1,408,453...1,424,197 JBrowse link
G SERPING1 serpin family G member 1 treatment ISO RGD PMID:8172580 RGD:8661646 NCBI chr 1:15,617,122...15,634,540
Ensembl chr 1:15,616,674...15,633,855 		JBrowse link
G SFTPB surfactant protein B ISO associated with Pneumonia;DNA:polymorphism: :1580C>T (human) RGD PMID:15190959 RGD:4143404 NCBI chr14:21,487,424...21,497,491
Ensembl chr14:21,488,387...21,499,850 		JBrowse link
G SOCS1 suppressor of cytokine signaling 1 severity ISO RGD PMID:19469017 RGD:150573701 NCBI chr 5:10,731,866...10,733,745
Ensembl chr 5:10,732,350...10,732,991 		JBrowse link
G TFPI tissue factor pathway inhibitor treatment ISO RGD PMID:11776329 RGD:11062085 NCBI chr10:73,004,762...73,105,772
Ensembl chr10:73,002,522...73,105,858 		JBrowse link
G THPO thrombopoietin ISO protein:increased expression:serum: RGD PMID:20467749 RGD:10449021 NCBI chr15:5,040,684...5,048,387 JBrowse link
G TNF tumor necrosis factor treatment ISO CTD Direct Evidence: marker/mechanism
protein:increased expression:peritoneal macrophage, cell surface (rat) 		CTD
RGD		 PMID:2213560 PMID:12622907 PMID:20054000 RGD:10449465 RGD:1598936
G TREM1 triggering receptor expressed on myeloid cells 1 ISO mRNA:decreased expression:polymorphonuclear leukocyte RGD PMID:24465168 RGD:126848796 NCBI chr17:30,873,647...30,885,292
Ensembl chr17:30,873,666...30,886,967 		JBrowse link
G ZC3H12A zinc finger CCCH-type containing 12A ISO RGD PMID:23422584 RGD:39938961 NCBI chr20:95,388,469...95,398,305
Ensembl chr20:95,388,477...95,397,960 		JBrowse link
trachoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CXCL8 C-X-C motif chemokine ligand 8 susceptibility ISO DNA:SNP:promoter:g.-251A>T (rs4073) (human) RGD PMID:20015396 RGD:150520200 NCBI chr 7:22,202,497...22,205,730
Ensembl chr 7:22,202,527...22,204,068 		JBrowse link
G IL10 interleukin 10 severity
no_association 		ISO DNA:SNP:promoter:−1082G>A (human)
DNA:SNP, haplotype:promoter:−1082G>A (human)
DNA:SNP:promoter:−819T>C, −592A>C (human)
DNA:haplotype: :
protein:increased expression:tear 		RGD PMID:11023480 PMID:15789056 PMID:17947295 PMID:18628987 RGD:7365037 RGD:7365053 RGD:7365072 RGD:7365085 NCBI chr25:22,590,389...22,595,877
Ensembl chr25:22,590,962...22,594,836 		JBrowse link
G IL17A interleukin 17A ISO mRNA:increased expression:conjunctiva (human) RGD PMID:21911461 RGD:9068420 NCBI chr17:20,314,082...20,319,917
Ensembl chr17:20,315,773...20,318,785 		JBrowse link
G TNF tumor necrosis factor ISO DNA:SNP, haplotypes:promoter:−308G>A (human) RGD PMID:17330135 RGD:8548830
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 chr16:43,134,648...43,152,313
Ensembl chr16:43,134,779...43,150,930 		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 chr11:7,501,562...7,536,332
Ensembl chr11:7,501,150...7,536,295 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 15420
    disease by infectious agent 2095
      Bacterial Infections and Mycoses 1023
        bacterial infectious disease 784
          commensal bacterial infectious disease 65
            Lemierre's syndrome 0
            Ritter's disease + 0
            actinobacillosis 0
            actinomycosis + 1
            chlamydia + 16
            gas gangrene 1
            inclusion conjunctivitis 0
            pertussis + 0
            toxic shock syndrome 54
            trachoma + 5
paths to the root