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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 emphysema
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Accession:DOID:9675 term browser browse the term
Definition:A chronic obstructive pulmonary disease that is characterized by permanent enlargement of air spaces distal to the terminal bronchioles and the destruction of the alveolar walls. (DO)
Synonyms:exact_synonym: Centriacinar Emphysema;   Centrilobular Emphysema;   Focal Emphysema;   Panacinar Emphysema;   Panacinar Emphysemas;   centriacinar emphysemas;   centrilobular emphysemas;   focal emphysemas;   panlobular emphysema;   panlobular emphysemas;   pulmonary emphysemas
 primary_id: MESH:D011656
 xref: EFO:0000464;   ICD10CM:J43.8;   ICD9CM:492.8



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pulmonary emphysema term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Adipoq adiponectin, C1Q and collagen domain containing ISO RGD PMID:20935231 RGD:5686887 NCBI chr11:91,226,524...91,240,244 JBrowse link
G Ager advanced glycosylation end product-specific receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:30659203 NCBI chr20:4,152,758...4,155,956 JBrowse link
G Alb albumin ISO RGD PMID:24365562 RGD:11035274 NCBI chr14:17,891,564...17,907,043 JBrowse link
G Bloc1s6 biogenesis of lysosomal organelles complex 1 subunit 6 ISS OMIM:130700 MouseDO NCBI chr 3:109,816,397...109,826,528 JBrowse link
G Ccl11 C-C motif chemokine ligand 11 disease_progression ISO associated with Pulmonary Disease, Chronic Obstructive;protein:increased expression:lung RGD PMID:17983873 RGD:4145393 NCBI chr10:67,525,975...67,530,576 JBrowse link
G Ccl2 C-C motif chemokine ligand 2 disease_progression ISO associated with Pulmonary Disease, Chronic Obstructive;protein:increased expression:sputum RGD PMID:20966041 RGD:4891458 NCBI chr10:67,503,077...67,504,875 JBrowse link
G Ccr5 C-C motif chemokine receptor 5 ISO mRNA, protein:increased expression:lung (mouse)
protein:increased expression:lung, lymphocyte (human)
RGD PMID:16284650 PMID:15526056 PMID:17883726 RGD:4892098, RGD:4892104, RGD:4892090 NCBI chr 8:132,629,097...132,660,980 JBrowse link
G Chi3l1 chitinase 3 like 1 ISO RGD PMID:20656949 RGD:4892658 NCBI chr13:45,641,802...45,649,787 JBrowse link
G Clptm1l CLPTM1-like severity ISO associated with smoking; DNA:SNP:intron:rs31489(human) RGD PMID:21622582 RGD:150530642 NCBI chr 1:29,667,545...29,683,530 JBrowse link
G Csf3 colony stimulating factor 3 treatment ISO RGD PMID:19537526 RGD:11039438 NCBI chr10:84,157,485...84,159,860 JBrowse link
G Cx3cl1 C-X3-C motif chemokine ligand 1 ISO RGD PMID:18772344 RGD:4891888 NCBI chr19:10,233,326...10,244,856 JBrowse link
G Cxcl1 C-X-C motif chemokine ligand 1 ISO mRNA:increased expression:lung RGD PMID:17023518 RGD:5135245 NCBI chr14:17,477,542...17,479,321 JBrowse link
G Cxcl10 C-X-C motif chemokine ligand 10 ISO protein:increased expression:lung, lymphocyte RGD PMID:15526056 RGD:4892104 NCBI chr14:15,989,066...15,991,263 JBrowse link
G Cxcl3 C-X-C motif chemokine ligand 3 ISO mRNA:increased expression:lung RGD PMID:17023518 RGD:5135245 NCBI chr14:17,571,900...17,573,624 JBrowse link
G Cxcl6 C-X-C motif chemokine ligand 6 ISO mRNA:increased expression:lung RGD PMID:17023518 RGD:5135245 NCBI chr14:17,310,790...17,312,250 JBrowse link
G Cxcl9 C-X-C motif chemokine ligand 9 ISO protein:increased expression:lung, lymphocyte RGD PMID:15526056 RGD:4892104 NCBI chr14:16,007,166...16,012,077 JBrowse link
G Cxcr3 C-X-C motif chemokine receptor 3 ISO RGD PMID:15526056 RGD:4892104 NCBI chr  X:66,844,318...66,846,969 JBrowse link
G Defb1 defensin beta 1 ISO mRNA:decreased expression:lung RGD PMID:18699806 RGD:4892249 NCBI chr16:70,298,862...70,313,604 JBrowse link
G Ednra endothelin receptor type A IMP RGD PMID:19897563 RGD:4892307 NCBI chr19:47,137,360...47,207,961 JBrowse link
G Egr1 early growth response 1 resistance ISO mRNA, protein:increased expression:lung (human)
associated with Tobacco Use Disorder;protein:increased expression:lung, epithelial cell (mouse)
RGD PMID:11021835 PMID:16601242 PMID:18830406 RGD:5131973, RGD:5131892, RGD:5131853 NCBI chr18:26,737,078...26,740,877 JBrowse link
G Elane elastase, neutrophil expressed IMP RGD PMID:12186827 RGD:10450557 NCBI chr 7:9,817,251...9,819,174 JBrowse link
G Eln elastin ISO CTD Direct Evidence: marker/mechanism CTD PMID:25106431 NCBI chr12:27,604,983...27,648,413 JBrowse link
G Ephx1 epoxide hydrolase 1 no_association
susceptibility
ISO associated with Pulmonary Disease, Chronic Obstructive;DNA:SNPs (human)
DNA:SNPs:exons:p.Y113H (rs1051740), p.H139R (rs2234922) (human)
DNA:SNP:exon:p.Y113H (rs1051740) (human)
CTD Direct Evidence: marker/mechanism
CTD
RGD
PMID:9288046 PMID:20525719 PMID:10853854 PMID:9288046 PMID:12579334 RGD:4140935, RGD:4889406, RGD:1601065, RGD:4889405 NCBI chr13:95,246,079...95,275,852 JBrowse link
G Fga fibrinogen alpha chain IEP protein:increased expression:plasma (rat) RGD PMID:20949089 RGD:11040553 NCBI chr 2:170,672,169...170,679,572 JBrowse link
G Fstl1 follistatin-like 1 ISS OMIM:130700 MouseDO NCBI chr11:62,895,391...62,948,581 JBrowse link
G Fut8 fucosyltransferase 8 ISS OMIM:130700 MouseDO NCBI chr 6:95,949,246...96,176,677 JBrowse link
G Gclc glutamate-cysteine ligase, catalytic subunit IDA RGD PMID:19879314 RGD:5134681 NCBI chr 8:87,510,251...87,548,896 JBrowse link
G Gstm1 glutathione S-transferase mu 1 susceptibility ISO DNA:deletion: : RGD PMID:20495862 RGD:4140927 NCBI chr 2:198,338,005...198,346,007 JBrowse link
G Gstm3 glutathione S-transferase mu 3 ISO RGD PMID:19723343 RGD:5135041 NCBI chr 2:195,590,450...195,612,578 JBrowse link
G Gstm5 glutathione S-transferase, mu 5 ISO RGD PMID:19723343 RGD:5135041 NCBI chr 2:195,531,599...195,534,562 JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO associated with Pulmonary Disease, Chronic Obstructive;DNA:SNP (human) RGD PMID:20525719 RGD:4140935 NCBI chr 1:210,767,237...210,770,242 JBrowse link
G Hdac2 histone deacetylase 2 treatment IEP
ISO
mRNA,proetin:increased expression,increased activity,hyperphosphorylation,hypercarbonylation:lung: RGD PMID:23326540 PMID:24040961 RGD:9590245, RGD:9590320 NCBI chr20:42,101,815...42,126,486 JBrowse link
G Hhip Hedgehog-interacting protein ISO DNA:haplotype insufficiency: : RGD PMID:25763110 RGD:11552596 NCBI chr19:27,863,684...27,952,528 JBrowse link
G Hmox1 heme oxygenase 1 susceptibility ISO CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:10631150 PMID:10631150 RGD:1601606 NCBI chr19:13,452,365...13,479,823 JBrowse link
G Il13 interleukin 13 ISO RGD PMID:11067861 RGD:4145652 NCBI chr10:38,290,926...38,293,483 JBrowse link
G Il17ra interleukin 17 receptor A ISO RGD PMID:21647421 RGD:5144212 NCBI chr 4:153,667,534...153,690,174 JBrowse link
G Il18 interleukin 18 ISO
IEP
mRNA, protein:increased expression:respiratory system fluid/secretion, macrophage RGD PMID:17400729 PMID:23392573 RGD:4889590, RGD:8655969 NCBI chr 8:59,802,072...59,829,275 JBrowse link
G Il1rl1 interleukin 1 receptor-like 1 treatment ISO associated with common cold; RGD PMID:30952808 RGD:40400740 NCBI chr 9:42,661,694...42,727,266 JBrowse link
G Itgb6 integrin subunit beta 6 ISO
ISS
CTD Direct Evidence: marker/mechanism
OMIM:130700
CTD
MouseDO
RGD
PMID:12634787 PMID:12634787 RGD:737734 NCBI chr 3:45,046,295...45,170,532 JBrowse link
G Jun Jun proto-oncogene, AP-1 transcription factor subunit ISS OMIM:130700 MouseDO NCBI chr 5:115,009,900...115,012,993 JBrowse link
G Keap1 Kelch-like ECH-associated protein 1 onset ISO protein:increased expression:lung (human) RGD PMID:18559366 PMID:19520915 RGD:5134973, RGD:6893395 NCBI chr 8:19,768,375...19,777,862 JBrowse link
G Kl Klotho ISS OMIM:130700 MouseDO NCBI chr12:490,402...531,417 JBrowse link
G Lox lysyl oxidase ISO ClinVar Annotator: match by term: Pulmonary emphysema ClinVar PMID:25741868 PMID:28492532 NCBI chr18:45,964,544...45,977,431 JBrowse link
G Mmp1 matrix metallopeptidase 1 ISO DNA:insertion:promoter:g.-1607insG rs1799750 (human) RGD PMID:17363767 RGD:4890375 NCBI chr 8:12,943,453...12,963,966 JBrowse link
G Mmp12 matrix metallopeptidase 12 ISO CTD Direct Evidence: marker/mechanism CTD PMID:12634787 PMID:25106431 NCBI chr 8:4,581,785...4,591,687 JBrowse link
G Mmp2 matrix metallopeptidase 2 IEP
ISO
protein:increased activity:lung
CTD Direct Evidence: marker/mechanism
CTD
RGD
PMID:25106431 PMID:19897563 RGD:4892307 NCBI chr19:30,327,643...30,355,856 JBrowse link
G Mmp9 matrix metallopeptidase 9 treatment IEP
ISO
protein:increased activity:lung
CTD Direct Evidence: marker/mechanism
CTD
RGD
PMID:25106431 PMID:19897563 PMID:18408070 PMID:14605041 RGD:4892307, RGD:5130151, RGD:8547887 NCBI chr 3:174,103,474...174,111,434 JBrowse link
G Mus81 MUS81 structure-specific endonuclease subunit ISS OMIM:130700 MouseDO NCBI chr 1:202,790,295...202,796,008 JBrowse link
G Nfe2l2 NFE2 like bZIP transcription factor 2 ISO protein:decreased expression:lung: RGD PMID:18559366 RGD:5134973 NCBI chr 3:81,001,529...81,031,165 JBrowse link
G Nfkbia NFKB inhibitor alpha treatment IDA RGD PMID:20472710 RGD:4891488 NCBI chr 6:78,593,844...78,597,307 JBrowse link
G Nos2 nitric oxide synthase 2 IEP
ISO
protein:increased expression:lung
mRNA,protein:increased expression:lung
RGD PMID:20472710 PMID:20956973 PMID:22000010 RGD:4891488, RGD:4891415, RGD:5509103 NCBI chr10:64,313,335...64,349,221 JBrowse link
G Nos3 nitric oxide synthase 3 ISO mRNA,protein:increased expression:lung RGD PMID:20956973 RGD:4891415 NCBI chr 4:11,686,088...11,706,604 JBrowse link
G Nqo1 NAD(P)H quinone dehydrogenase 1 ISO mRNA:decreased expression:lung RGD PMID:18559366 RGD:5134973 NCBI chr19:52,205,374...52,220,267 JBrowse link
G Pgf placental growth factor ISO mRNA, protein:increased expression:lung, plasma RGD PMID:17023518 RGD:5135245 NCBI chr 6:110,547,165...110,557,747 JBrowse link
G Ppargc1a PPARG coactivator 1 alpha ISO RGD PMID:23144332 RGD:7242020 NCBI chr14:63,073,505...63,729,215 JBrowse link
G Ptgs2 prostaglandin-endoperoxide synthase 2 IMP RGD PMID:20472710 RGD:4891488 NCBI chr13:64,714,063...64,722,320 JBrowse link
G Ptma prothymosin alpha ISS OMIM:130700 MouseDO NCBI chr 9:94,624,194...94,628,276 JBrowse link
G Scnn1b sodium channel epithelial 1 subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:27982104 NCBI chr 1:185,861,326...185,915,717 JBrowse link
G Serpina1 serpin family A member 1 ISO CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:3485249 PMID:21030517 PMID:19941265 RGD:4892126, RGD:4892125 NCBI chr 6:128,631,101...128,653,125 JBrowse link
G Sftpc surfactant protein C susceptibility ISO DNA:polymorphism: :138A>C, 186A>G (human) RGD PMID:18038590 RGD:4144115 NCBI chr15:45,596,565...45,599,615 JBrowse link
G Smo smoothened, frizzled class receptor ISS OMIM:130700 MouseDO NCBI chr 4:59,311,084...59,341,280 JBrowse link
G Smpd3 sphingomyelin phosphodiesterase 3 ISO protein:increased expression:lung: RGD PMID:20448054 RGD:10041059 NCBI chr19:34,162,337...34,245,786 JBrowse link
G Srfbp1 serum response factor binding protein 1 ISO ClinVar Annotator: match by term: Pulmonary emphysema ClinVar PMID:25741868 PMID:28492532 NCBI chr18:45,920,389...45,945,385 JBrowse link
G Tacr1 tachykinin receptor 1 ISO RGD PMID:19445658 RGD:5147818 NCBI chr 4:116,478,617...116,647,492 JBrowse link
G Tgfb1 transforming growth factor, beta 1 severity ISO associated with Pulmonary Disease, Chronic Obstructive;DNA:SNPs:promoter:rs1800469, rs1982073 (human)
CTD Direct Evidence: therapeutic
CTD
RGD
PMID:12634787 PMID:18670143 RGD:4145272 NCBI chr 1:90,324,312...90,340,627 JBrowse link
G Tlr2 toll-like receptor 2 ISO protein:increased expression:alveolar macrophage RGD PMID:18399852 RGD:4145342 NCBI chr 2:171,499,189...171,504,831 JBrowse link
G Tlr4 toll-like receptor 4 ISO
ISS
OMIM:130700 MouseDO
RGD
PMID:17053835 RGD:4144170 NCBI chr 5:85,161,247...85,174,882 JBrowse link
G Tnf tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:25106431 NCBI chr20:3,626,685...3,629,303 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19139
    Pathological Conditions, Signs and Symptoms 13623
      Pathologic Processes 8325
        Emphysema 84
          pulmonary emphysema 68
            Berry Aneurysm, Cirrhosis, Pulmonary Emphysema, and Cerebral Calcification 0
            Congenital Lobar Emphysema 0
            Hereditary Pulmonary Emphysema + 0
Path 2
Term Annotations click to browse term
  disease 19139
    disease of anatomical entity 18450
      respiratory system disease 5242
        lower respiratory tract disease 2354
          lung disease 2315
            obstructive lung disease 481
              chronic obstructive pulmonary disease 245
                pulmonary emphysema 68
                  Berry Aneurysm, Cirrhosis, Pulmonary Emphysema, and Cerebral Calcification 0
                  Congenital Lobar Emphysema 0
                  Hereditary Pulmonary Emphysema + 0
paths to the root