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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 chr34:19,398,310...19,410,519
Ensembl chr34:19,354,825...19,409,844 		JBrowse link
G AGER advanced glycosylation end-product specific receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:30659203 NCBI chr12:1,574,251...1,577,410
Ensembl chr12:1,574,251...1,577,129 		JBrowse link
G ALB albumin ISO RGD PMID:24365562 RGD:11035274 NCBI chr13:62,133,747...62,169,349
Ensembl chr13:62,053,814...62,294,709 		JBrowse link
G B9D2 B9 domain containing 2 severity ISO CTD Direct Evidence: therapeutic
associated with Pulmonary Disease, Chronic Obstructive;DNA:SNPs:promoter:rs1800469, rs1982073 (human)		 CTD
RGD		 PMID:12634787 PMID:18670143 RGD:4145272 NCBI chr 1:112,621,832...112,627,726
Ensembl chr 1:112,621,633...112,643,885 		JBrowse link
G BLOC1S6 biogenesis of lysosomal organelles complex 1 subunit 6 ISO OMIM:130700 MouseDO NCBI chr30:11,861,119...11,949,451
Ensembl chr30:11,811,339...11,937,353 		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 chr 9:39,008,187...39,009,932 JBrowse link
G CCR5 C-C motif chemokine receptor 5 ISO protein:increased expression:lung, lymphocyte (human)
mRNA, protein:increased expression:lung (mouse)		 RGD PMID:15526056 PMID:16284650 PMID:17883726 RGD:4892090 RGD:4892098 RGD:4892104 NCBI chr20:42,293,288...42,297,952
Ensembl chr20:42,294,996...42,297,952 		JBrowse link
G CHI3L1 chitinase 3 like 1 ISO RGD PMID:20656949 RGD:4892658 NCBI chr 7:25,620...32,954
Ensembl chr 7:26,316...33,427 		JBrowse link
G CLPTM1L CLPTM1 like severity ISO associated with smoking; DNA:SNP:intron:rs31489(human) RGD PMID:21622582 RGD:150530642 NCBI chr34:11,263,274...11,277,666
Ensembl chr34:11,263,162...11,277,436 		JBrowse link
G CSF3 colony stimulating factor 3 treatment ISO RGD PMID:19537526 RGD:11039438 NCBI chr 9:22,529,643...22,532,326
Ensembl chr 9:22,530,698...22,533,108 		JBrowse link
G CX3CL1 C-X3-C motif chemokine ligand 1 ISO RGD PMID:18772344 RGD:4891888 NCBI chr 2:59,022,794...59,032,095
Ensembl chr 2:59,022,794...59,032,095 		JBrowse link
G CXCL10 C-X-C motif chemokine ligand 10 ISO protein:increased expression:lung, lymphocyte RGD PMID:15526056 RGD:4892104 NCBI chr32:598,406...599,925
Ensembl chr32:597,987...599,979 		JBrowse link
G CXCR3 C-X-C motif chemokine receptor 3 ISO RGD PMID:15526056 RGD:4892104 NCBI chr  X:55,882,433...55,884,582
Ensembl chr  X:55,882,433...55,884,582 		JBrowse link
G CYP2A7 cytochrome P450, family 2, subfamily A, polypeptide 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:12832682 NCBI chr 1:112,900,508...112,906,745
Ensembl chr 1:112,900,403...112,907,076 		JBrowse link
G DEFB1 defensin beta 1 ISO mRNA:decreased expression:lung RGD PMID:18699806 RGD:4892249 NCBI chr16:58,871,018...58,881,592
Ensembl chr16:58,871,018...58,881,592 		JBrowse link
G EDNRA endothelin receptor type A ISO RGD PMID:19897563 RGD:4892307 NCBI chr15:45,823,472...45,878,527
Ensembl chr15:45,823,560...45,876,463 		JBrowse link
G EGR1 early growth response 1 resistance ISO associated with Tobacco Use Disorder;protein:increased expression:lung, epithelial cell (mouse)
mRNA, protein:increased expression:lung (human)		 RGD PMID:11021835 PMID:16601242 PMID:18830406 RGD:5131853 RGD:5131892 RGD:5131973 NCBI chr11:26,046,195...26,049,806
Ensembl chr11:26,046,228...26,048,575 		JBrowse link
G ELANE elastase, neutrophil expressed ISO RGD PMID:12186827 RGD:10450557 NCBI chr20:57,789,044...57,790,932
Ensembl chr20:57,788,062...57,790,932 		JBrowse link
G ELN elastin ISO CTD Direct Evidence: marker/mechanism CTD PMID:25106431 NCBI chr 6:6,299,524...6,331,425
Ensembl chr 6:6,300,727...6,331,325 		JBrowse link
G EPHX1 epoxide hydrolase 1 no_association
susceptibility		 ISO DNA:SNPs:exons:p.Y113H (rs1051740), p.H139R (rs2234922) (human)
CTD Direct Evidence: marker/mechanism
DNA:SNP:exon:p.Y113H (rs1051740) (human)
associated with Pulmonary Disease, Chronic Obstructive;DNA:SNPs (human)		 RGD
CTD		 PMID:9288046 PMID:10853854 PMID:12579334 PMID:20525719 RGD:1601065 RGD:4140935 RGD:4889405 RGD:4889406 NCBI chr 7:38,964,319...39,004,902
Ensembl chr 7:38,964,338...38,999,238 		JBrowse link
G FGA fibrinogen alpha chain ISO protein:increased expression:plasma (rat) RGD PMID:20949089 RGD:11040553 NCBI chr15:52,238,305...52,247,017
Ensembl chr15:52,236,198...52,246,975 		JBrowse link
G FSTL1 follistatin like 1 ISO OMIM:130700 MouseDO NCBI chr33:23,892,317...23,914,406
Ensembl chr33:23,894,573...23,933,779 		JBrowse link
G FUT8 fucosyltransferase 8 ISO OMIM:130700 MouseDO NCBI chr 8:39,670,629...39,972,729
Ensembl chr 8:39,825,246...39,972,612 		JBrowse link
G GCLC glutamate-cysteine ligase catalytic subunit ISO RGD PMID:19879314 RGD:5134681 NCBI chr12:20,999,815...21,047,779
Ensembl chr12:21,000,792...21,047,779 		JBrowse link
G GSTM3 glutathione S-transferase mu 3 ISO RGD PMID:19723343 RGD:5135041 NCBI chr 6:42,187,869...42,191,274
Ensembl chr 6:42,187,967...42,191,273 		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 chr18:49,905,161...49,908,182
Ensembl chr18:49,905,161...49,908,182 		JBrowse link
G HDAC2 histone deacetylase 2 treatment ISO mRNA,proetin:increased expression,increased activity,hyperphosphorylation,hypercarbonylation:lung: RGD PMID:23326540 PMID:24040961 RGD:9590245 RGD:9590320 NCBI chr12:70,053,822...70,083,491
Ensembl chr12:70,053,297...70,103,578 		JBrowse link
G HHIP hedgehog interacting protein ISO DNA:haplotype insufficiency: : RGD PMID:25763110 RGD:11552596 NCBI chr15:43,432,464...43,525,973
Ensembl chr15:43,431,650...43,520,861 		JBrowse link
G HMOX1 heme oxygenase 1 susceptibility ISO CTD Direct Evidence: marker/mechanism
DNA:allele:promoter:L allele of the (GT)n repeat (>30 repeats)		 CTD
RGD		 PMID:10631150 RGD:1601606 NCBI chr10:28,744,404...28,751,544
Ensembl chr10:28,743,795...28,751,773 		JBrowse link
G IL13 interleukin 13 ISO RGD PMID:11067861 RGD:4145652 NCBI chr11:20,957,870...20,961,391
Ensembl chr11:20,958,464...20,961,388 		JBrowse link
G IL17RA interleukin 17 receptor A ISO RGD PMID:21647421 RGD:5144212 NCBI chr27:44,798,960...44,812,287
Ensembl chr27:44,791,066...44,811,064 		JBrowse link
G IL18 interleukin 18 ISO mRNA, protein:increased expression:respiratory system fluid/secretion, macrophage RGD PMID:17400729 PMID:23392573 RGD:4889590 RGD:8655969 NCBI chr 5:20,972,742...20,995,327
Ensembl chr 5:20,972,871...20,995,348 		JBrowse link
G IL1RL1 interleukin 1 receptor like 1 treatment ISO associated with common cold; RGD PMID:30952808 RGD:40400740 NCBI chr10:40,658,191...40,732,097
Ensembl chr10:40,659,041...40,677,357 		JBrowse link
G ITGB6 integrin subunit beta 6 ISO CTD Direct Evidence: marker/mechanism
OMIM:130700		 CTD
RGD
MouseDO		 PMID:12634787 RGD:737734 NCBI chr36:5,833,206...5,962,699
Ensembl chr36:5,834,638...5,962,633 		JBrowse link
G JUN Jun proto-oncogene, AP-1 transcription factor subunit ISO OMIM:130700 MouseDO NCBI chr 5:50,966,698...50,968,939 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 chr20:50,651,070...50,661,178
Ensembl chr20:50,650,711...50,658,496 		JBrowse link
G KL klotho ISO OMIM:130700 MouseDO NCBI chr25:7,154,359...7,201,744
Ensembl chr25:7,156,620...7,199,558 		JBrowse link
G LOX lysyl oxidase ISO ClinVar Annotator: match by term: Pulmonary emphysema ClinVar PMID:25741868 PMID:28492532 NCBI chr11:12,023,645...12,040,015
Ensembl chr11:12,027,250...12,039,819 		JBrowse link
G MMP1 matrix metallopeptidase 1 ISO DNA:insertion:promoter:g.-1607insG rs1799750 (human) RGD PMID:17363767 RGD:4890375 NCBI chr 5:28,978,385...28,986,644
Ensembl chr 5:28,978,473...28,986,648 		JBrowse link
G MMP12 matrix metallopeptidase 12 ISO CTD Direct Evidence: marker/mechanism CTD PMID:12634787 PMID:25106431 NCBI chr 5:28,918,626...28,933,404
Ensembl chr 5:28,918,594...28,933,309 		JBrowse link
G MMP2 matrix metallopeptidase 2 ISO protein:increased activity:lung
CTD Direct Evidence: marker/mechanism		 RGD
CTD		 PMID:19897563 PMID:25106431 RGD:4892307 NCBI chr 2:60,471,092...60,492,991
Ensembl chr 2:60,471,257...60,494,113 		JBrowse link
G MMP9 matrix metallopeptidase 9 treatment ISO protein:increased activity:lung
CTD Direct Evidence: marker/mechanism		 RGD
CTD		 PMID:14605041 PMID:18408070 PMID:19897563 PMID:25106431 RGD:4892307 RGD:5130151 RGD:8547887 NCBI chr24:33,274,260...33,281,116
Ensembl chr24:33,274,268...33,281,293 		JBrowse link
G MUS81 MUS81 structure-specific endonuclease subunit ISO OMIM:130700 MouseDO NCBI chr18:51,396,980...51,404,563
Ensembl chr18:51,396,980...51,402,534 		JBrowse link
G NFE2L2 NFE2 like bZIP transcription factor 2 ISO protein:decreased expression:lung: RGD PMID:18559366 RGD:5134973 NCBI chr36:20,989,205...21,087,044
Ensembl chr36:20,989,360...21,012,524 		JBrowse link
G NFKBIA NFKB inhibitor alpha treatment ISO RGD PMID:20472710 RGD:4891488 NCBI chr 8:14,100,203...14,103,453
Ensembl chr 8:14,100,671...14,103,433 		JBrowse link
G NOS2 nitric oxide synthase 2 ISO mRNA,protein:increased expression:lung RGD PMID:20472710 PMID:20956973 PMID:22000010 RGD:4891415 RGD:4891488 RGD:5509103 NCBI chr 9:42,171,821...42,210,217
Ensembl chr 9:42,171,821...42,208,588 		JBrowse link
G NOS3 nitric oxide synthase 3 ISO mRNA,protein:increased expression:lung RGD PMID:20956973 RGD:4891415 NCBI chr16:15,054,196...15,072,454
Ensembl chr16:15,011,344...15,072,277 		JBrowse link
G NQO1 NAD(P)H quinone dehydrogenase 1 ISO mRNA:decreased expression:lung RGD PMID:18559366 RGD:5134973 NCBI chr 5:79,979,593...79,990,875
Ensembl chr 5:79,978,865...79,989,860 		JBrowse link
G PGF placental growth factor ISO mRNA, protein:increased expression:lung, plasma RGD PMID:17023518 RGD:5135245 NCBI chr 8:48,059,554...48,110,534
Ensembl chr 8:48,059,552...48,075,170 		JBrowse link
G PPARGC1A PPARG coactivator 1 alpha ISO RGD PMID:23144332 RGD:7242020 NCBI chr 3:85,645,942...86,284,570
Ensembl chr 3:86,016,140...86,281,269 		JBrowse link
G PTGS2 prostaglandin-endoperoxide synthase 2 ISO RGD PMID:20472710 RGD:4891488 NCBI chr 7:19,668,079...19,674,903
Ensembl chr 7:19,668,082...19,674,903 		JBrowse link
G PTMA prothymosin alpha ISO OMIM:130700 MouseDO NCBI chr25:43,563,145...43,567,987
Ensembl chr25:43,562,395...43,675,699 		JBrowse link
G SCNN1B sodium channel epithelial 1 subunit beta ISO CTD Direct Evidence: marker/mechanism CTD PMID:27982104 NCBI chr 6:22,439,643...22,481,349
Ensembl chr 6:22,439,643...22,481,349 		JBrowse link
G SERPINA1 serpin family A member 1 ISO CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:3485249 PMID:19941265 PMID:21030517 RGD:4892125 RGD:4892126 NCBI chr 8:63,388,498...63,400,377
Ensembl chr 8:63,376,945...63,398,435 		JBrowse link
G SFTPC surfactant protein C susceptibility ISO DNA:polymorphism: :138A>C, 186A>G (human) RGD PMID:18038590 RGD:4144115 NCBI chr25:35,088,295...35,090,995
Ensembl chr25:35,088,279...35,091,457 		JBrowse link
G SMO smoothened, frizzled class receptor ISO OMIM:130700 MouseDO NCBI chr14:7,518,871...7,527,703
Ensembl chr14:7,518,856...7,528,033 		JBrowse link
G SMPD3 sphingomyelin phosphodiesterase 3 ISO protein:increased expression:lung: RGD PMID:20448054 RGD:10041059 NCBI chr 5:81,089,657...81,172,173
Ensembl chr 5:81,142,888...81,172,189 		JBrowse link
G SRFBP1 serum response factor binding protein 1 ISO ClinVar Annotator: match by term: Pulmonary emphysema ClinVar PMID:25741868 PMID:28492532 NCBI chr11:11,937,274...12,001,841
Ensembl chr11:11,940,280...12,000,962 		JBrowse link
G TACR1 tachykinin receptor 1 ISO RGD PMID:19445658 RGD:5147818 NCBI chr17:48,038,010...48,178,971
Ensembl chr17:48,038,010...48,178,971 		JBrowse link
G TLR2 toll like receptor 2 ISO protein:increased expression:alveolar macrophage RGD PMID:18399852 RGD:4145342 NCBI chr15:51,454,557...51,465,429
Ensembl chr15:51,454,695...51,465,241 		JBrowse link
G TLR4 toll like receptor 4 ISO OMIM:130700 RGD
MouseDO		 PMID:17053835 RGD:4144170 NCBI chr11:71,356,390...71,367,166
Ensembl chr11:71,356,390...71,367,165 		JBrowse link
G TNF tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:25106431 NCBI chr12:1,074,561...1,076,425
Ensembl chr12:1,074,552...1,076,425 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 15603
    Pathological Conditions, Signs and Symptoms 12031
      Pathologic Processes 7491
        Emphysema 78
          pulmonary emphysema 62
            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 15603
    disease of anatomical entity 15182
      respiratory system disease 3399
        lower respiratory tract disease 2203
          lung disease 2166
            obstructive lung disease 453
              chronic obstructive pulmonary disease 228
                pulmonary emphysema 62
                  Berry Aneurysm, Cirrhosis, Pulmonary Emphysema, and Cerebral Calcification 0
                  Congenital Lobar Emphysema 0
                  Hereditary Pulmonary Emphysema + 0
paths to the root