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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:idiopathic pulmonary fibrosis
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Accession:DOID:0050156 term browser browse the term
Definition:A pulmonary fibrosis that is characterized by scarring of the lung characterized by stiffness in the lungs and makes it difficult to breathe. (DO)
Synonyms:exact_synonym: IPF;   Idiopathic Fibrosing Alveolitis, Chronic Form;   cryptogenic fibrosing alveolitis;   familial idiopathic pulmonary fibrosis;   fibrocystic pulmonary dysplasia;   fibrocystic pulmonary dysplasias;   idiopathic pulmonary fibroses
 narrow_synonym: Hamman Rich disease;   UIP Hamman Rich disease
 broad_synonym: SFTPA2-related condition
 related_synonym: idiopathic pulmonary fibrosis, susceptibility to;   usual interstitial pneumonia;   usual interstitial pneumonias;   usual interstitial pneumonitis
 xref: EFO:0000768;   GARD:8609;   ICD10CM:J84.112;   ICD9CM:516.31;   MESH:D054990;   NCI:C35715;   NCI:C35716


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idiopathic pulmonary fibrosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abca3 ATP binding cassette subfamily A member 3 ISO ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia ClinVar PMID:15976379 PMID:17597647 PMID:18246475 PMID:18317237 PMID:18603241 More... NCBI chr10:13,886,948...13,944,286
Ensembl chr10:13,887,083...13,944,285 		JBrowse link
G Akt1 AKT serine/threonine kinase 1 ISO mRNA:increased expression:blood plasma (human) RGD PMID:31874165 RGD:152995482 NCBI chr 6:137,534,810...137,555,131
Ensembl chr 6:137,535,390...137,552,610 		JBrowse link
G Apoa1 apolipoprotein A1 ISO protein: decreased expression: respiratory system fluid/secretion RGD PMID:20463180 RGD:5508222 NCBI chr 8:55,423,945...55,425,729
Ensembl chr 8:55,423,825...55,425,729 		JBrowse link
G Atp11a ATPase phospholipid transporting 11A ISO CTD Direct Evidence: marker/mechanism CTD PMID:23583980 NCBI chr16:83,359,884...83,469,807
Ensembl chr16:83,359,884...83,469,767 		JBrowse link
G Bmp1 bone morphogenetic protein 1 ISO ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia ClinVar PMID:24033266 PMID:25741868 PMID:28492532 NCBI chr15:51,961,310...52,005,597
Ensembl chr15:51,961,310...52,005,485 		JBrowse link
G Brd4 bromodomain containing 4 ISO RGD PMID:23759512 RGD:9586353 NCBI chr 7:11,866,997...11,946,575
Ensembl chr 7:11,866,997...11,946,923 		JBrowse link
G Ccl12 C-C motif chemokine ligand 12 ISO CTD Direct Evidence: therapeutic CTD PMID:28434932 NCBI chr10:67,567,876...67,569,426
Ensembl chr10:67,567,876...67,569,426 		JBrowse link
G Cflar CASP8 and FADD-like apoptosis regulator ISO mRNA,protein:increased expression:lung myofibroblast: RGD PMID:22582174 RGD:11341695 NCBI chr 9:67,679,502...67,747,226
Ensembl chr 9:67,679,559...67,726,434 		JBrowse link
G Cxcl6 C-X-C motif chemokine ligand 6 ISO DNA:polymorphism:promoter:-156G>C (human)
protein:increased expression:lung, macrophage, type II pneumocyte 		RGD PMID:20137269 PMID:11751193 RGD:5135241, RGD:5135250 NCBI chr14:17,594,959...17,596,417
Ensembl chr14:17,594,959...17,596,417 		JBrowse link
G Ddr1 discoidin domain receptor tyrosine kinase 1 treatment ISO
IMP 		mRNA:increased expression:lung (human) RGD PMID:30119248 PMID:30119248 RGD:151347411, RGD:151347411 NCBI chr20:3,047,269...3,069,277
Ensembl chr20:3,050,375...3,069,276 		JBrowse link
G Dpp9 dipeptidyl peptidase 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:23583980 NCBI chr 9:1,098,505...1,133,500
Ensembl chr 9:1,095,929...1,177,715 		JBrowse link
G Dsp desmoplakin ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia 		CTD
ClinVar		 PMID:23583980 NCBI chr17:26,829,153...26,877,419
Ensembl chr17:26,829,153...26,877,121 		JBrowse link
G Ehmt2 euchromatic histone lysine methyltransferase 2 ISO RGD PMID:24652950 RGD:9589169 NCBI chr20:3,924,263...3,941,238
Ensembl chr20:3,924,263...3,941,384 		JBrowse link
G Ep300 E1A binding protein p300 treatment ISO
IMP 		mRNA:increased expression:lung (human) RGD PMID:30119248 PMID:30119248 RGD:151347411, RGD:151347411 NCBI chr 7:114,987,857...115,058,652
Ensembl chr 7:114,946,982...115,058,574 		JBrowse link
G Esr1 estrogen receptor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30165855 NCBI chr 1:43,511,685...43,904,454
Ensembl chr 1:43,644,392...43,900,354 		JBrowse link
G F3 coagulation factor III, tissue factor ISO protein:increased expression:respiratory system fluid/secretion RGD PMID:10946084 RGD:11060143 NCBI chr 2:212,511,675...212,523,375
Ensembl chr 2:212,511,680...212,523,369 		JBrowse link
G Fam13a family with sequence similarity 13, member A ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia 		CTD
ClinVar		 PMID:23583980 NCBI chr 4:89,386,685...89,485,940
Ensembl chr 4:89,388,569...89,485,988 		JBrowse link
G Fas Fas cell surface death receptor ISO RGD PMID:15148335 RGD:11049166 NCBI chr 1:241,212,155...241,245,774
Ensembl chr 1:241,205,935...241,246,104 		JBrowse link
G Faslg Fas ligand ISO RGD PMID:15148335 RGD:11049166 NCBI chr13:76,680,885...76,706,042
Ensembl chr13:76,688,243...76,695,503 		JBrowse link
G Fgfr2 fibroblast growth factor receptor 2 ISO protein:increased expression:lung (human) RGD PMID:29722558 RGD:155791445 NCBI chr 1:194,175,703...194,280,914
Ensembl chr 1:194,175,705...194,280,914 		JBrowse link
G Fosl2 FOS like 2, AP-1 transcription factor subunit ISS OMIM:178500 MouseDO NCBI chr 6:30,017,952...30,039,269
Ensembl chr 6:30,021,916...30,039,406 		JBrowse link
G Gper1 G protein-coupled estrogen receptor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:30165855 NCBI chr12:20,331,073...20,336,527
Ensembl chr12:20,327,679...20,337,144 		JBrowse link
G Hif1a hypoxia inducible factor 1 subunit alpha ISO CTD Direct Evidence: therapeutic CTD PMID:28434932 NCBI chr 6:98,357,788...98,405,068
Ensembl chr 6:98,359,910...98,405,323 		JBrowse link
G Il1rl1 interleukin 1 receptor-like 1 ISO protein:increased expression:serum RGD PMID:14555548 RGD:5144236 NCBI chr 9:50,157,326...50,222,888
Ensembl chr 9:50,204,551...50,222,891 		JBrowse link
G Il2ra interleukin 2 receptor subunit alpha ISO RGD PMID:21309737 RGD:5147438 NCBI chr17:71,759,802...71,808,475
Ensembl chr17:71,759,802...71,808,507 		JBrowse link
G Mir184 microRNA 184 ISO RNA:decreased expression:blood plasma (human) RGD PMID:31874165 RGD:152995482 NCBI chr 8:99,222,982...99,223,058 JBrowse link
G Mir31 microRNA 31 ISO RNA:increased expression:blood plasma (human) RGD PMID:31874165 RGD:152995482 NCBI chr 5:108,714,849...108,714,954 JBrowse link
G Mmp1 matrix metallopeptidase 1 ISO protein:increased expression:lung,bronchoalveolar lavage fluid: RGD PMID:18447576 RGD:4890373 NCBI chr 8:12,943,453...12,963,966
Ensembl chr 8:12,943,453...12,963,964 		JBrowse link
G Mmp3 matrix metallopeptidase 3 ISO mRNA, protein:increased expression:lung
CTD Direct Evidence: therapeutic 		CTD
RGD		 PMID:28434932 PMID:21871427 RGD:8694097 NCBI chr 8:12,925,267...12,938,828
Ensembl chr 8:12,925,280...12,938,826 		JBrowse link
G Muc1 mucin 1, cell surface associated ISO protein:increased expression:serum: RGD PMID:22963039 RGD:7244290 NCBI chr 2:176,933,312...176,938,497
Ensembl chr 2:176,933,047...176,938,491 		JBrowse link
G Muc5b mucin 5B, oligomeric mucus/gel-forming ISO ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia
CTD Direct Evidence: marker/mechanism 		ClinVar
CTD		 PMID:21506741 PMID:21506748 PMID:23321605 PMID:23583980 PMID:23692170 More... NCBI chr 1:206,346,400...206,378,367
Ensembl chr 1:206,346,400...206,378,367 		JBrowse link
G Ntrk2 neurotrophic receptor tyrosine kinase 2 ISO mRNA:increased expression:lung RGD PMID:21330466 RGD:5684550 NCBI chr17:5,560,558...5,875,899
Ensembl chr17:5,564,570...5,874,628 		JBrowse link
G Parn poly(A)-specific ribonuclease ISO CTD Direct Evidence: marker/mechanism CTD PMID:25848748 NCBI chr10:1,917,830...2,055,749
Ensembl chr10:1,917,830...2,055,722 		JBrowse link
G Parp1 poly (ADP-ribose) polymerase 1 ISO mRNA,protein:increased expression, increased activity:fibroblast RGD PMID:23260200 RGD:10413908 NCBI chr13:94,839,484...94,871,295
Ensembl chr13:94,839,433...94,871,567 		JBrowse link
G Plau plasminogen activator, urokinase ISO CTD Direct Evidence: therapeutic CTD PMID:18491991 NCBI chr15:3,505,485...3,511,987
Ensembl chr15:3,505,487...3,512,030 		JBrowse link
G Ptgs2 prostaglandin-endoperoxide synthase 2 ISO DNA:SNPs: :3050G>C, 8473C>T (human)
protein:decreased expression:lung: 		RGD PMID:21319594 PMID:20203246 PMID:14511257 RGD:5135280, RGD:5135461, RGD:5135507 NCBI chr13:64,714,063...64,722,320
Ensembl chr13:64,713,619...64,722,320 		JBrowse link
G RT1-Db1 RT1 class II, locus Db1 susceptibility ISO DNA:polymorphism (human) RGD PMID:21373184 RGD:5147566 NCBI chr20:4,550,594...4,560,182
Ensembl chr20:4,550,596...4,560,165 		JBrowse link
G Rtel1 regulator of telomere elongation helicase 1 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia 		CTD
ClinVar		 PMID:25607374 PMID:25741868 PMID:25848748 PMID:28492532 NCBI chr 3:188,778,329...188,842,877
Ensembl chr 3:188,807,951...188,843,709 		JBrowse link
G Setd2 SET domain containing 2, histone lysine methyltransferase exacerbates ISO associated with lung squamous cell carcinoma; DNA:mutations:multiple (human) RGD PMID:33533494 RGD:150429642 NCBI chr 8:119,390,207...119,475,863
Ensembl chr 8:119,390,207...119,475,863 		JBrowse link
G Sftpa1 surfactant protein A1 ISO ClinVar Annotator: match by term: Pulmonary fibrosis, idiopathic, susceptibility to ClinVar PMID:13680361 PMID:24033266 PMID:25741868 NCBI chr16:17,042,264...17,045,770
Ensembl chr16:17,042,255...17,045,769 		JBrowse link
G Sftpc surfactant protein C ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia 		CTD
ClinVar		 PMID:14735158 PMID:15039969 PMID:15516475 PMID:15709974 PMID:18383112 More... NCBI chr15:52,006,274...52,009,324
Ensembl chr15:52,006,283...52,009,475 		JBrowse link
G Smad2 SMAD family member 2 ISO mRNA:increased expression:blood plasma (human) RGD PMID:31874165 RGD:152995482 NCBI chr18:72,124,792...72,193,345
Ensembl chr18:72,124,863...72,187,388 		JBrowse link
G Smad6 SMAD family member 6 ISO mRNA:decreased expression:blood plasma (human) RGD PMID:31874165 RGD:152995482 NCBI chr 8:73,345,457...73,414,985
Ensembl chr 8:73,345,460...73,414,149 		JBrowse link
G St14 ST14 transmembrane serine protease matriptase ISO CTD Direct Evidence: marker/mechanism CTD PMID:26599507 NCBI chr 8:37,798,994...37,839,881
Ensembl chr 8:37,798,995...37,855,652 		JBrowse link
G Stat3 signal transducer and activator of transcription 3 ISO CTD Direct Evidence: marker/mechanism CTD
RGD		 PMID:30481203 PMID:22684844 RGD:6892915 NCBI chr10:86,311,528...86,363,513
Ensembl chr10:86,311,535...86,363,359 		JBrowse link
G Stn1 STN1 subunit of CST complex ISO CTD Direct Evidence: marker/mechanism CTD PMID:23583980 NCBI chr 1:256,336,916...256,371,143
Ensembl chr 1:256,315,367...256,370,736 		JBrowse link
G Terc telomerase RNA component ISO CTD Direct Evidence: marker/mechanism CTD PMID:17392301 PMID:17460043 PMID:23535734 NCBI chr 2:114,744,148...114,744,535 JBrowse link
G Tert telomerase reverse transcriptase ISO DNA:deletion, missense mutations, splice-site mutations:multiple
CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia | ClinVar Annotator: match by term: Idiopathic Pulmonary Fibrosis | ClinVar Annotator: match by term: Idiopathic fibrosing alveolitis, chronic form 		CTD
ClinVar
RGD		 PMID:9536098 PMID:15814878 PMID:15885610 PMID:16247010 PMID:16627250 More... RGD:11038666 NCBI chr 1:31,465,766...31,488,650
Ensembl chr 1:31,466,056...31,488,111 		JBrowse link
G Tfpi tissue factor pathway inhibitor severity ISO protein:increased expression:Bronchoalveolar lavage,epithelial cell: RGD PMID:10946084 RGD:11060143 NCBI chr 3:89,939,862...89,989,253
Ensembl chr 3:89,939,868...89,980,742 		JBrowse link
G Thbd thrombomodulin severity ISO RGD PMID:20418386 RGD:5685036 NCBI chr 3:156,316,526...156,320,178
Ensembl chr 3:156,306,632...156,320,582 		JBrowse link
G Tnf tumor necrosis factor ISO
ISS 		CTD Direct Evidence: marker/mechanism
OMIM:178500 		CTD
MouseDO		 PMID:8473757 NCBI chr20:3,626,685...3,629,303
Ensembl chr20:3,626,532...3,629,303 		JBrowse link
G Tollip toll interacting protein ISO ClinVar Annotator: match by term: Fibrocystic pulmonary dysplasia ClinVar NCBI chr 1:206,391,120...206,413,809
Ensembl chr 1:206,380,308...206,411,988 		JBrowse link
G Wnt5a Wnt family member 5A ISO CTD Direct Evidence: marker/mechanism CTD PMID:28726637 NCBI chr16:3,702,300...3,724,860
Ensembl chr16:3,703,665...3,724,860 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19167
    Pathological Conditions, Signs and Symptoms 13667
      Pathologic Processes 8430
        Fibrosis 1597
          pulmonary fibrosis 230
            idiopathic pulmonary fibrosis 53
Path 2
Term Annotations click to browse term
  disease 19167
    disease of anatomical entity 18473
      respiratory system disease 5247
        lower respiratory tract disease 2352
          lung disease 2314
            interstitial lung disease 547
              pulmonary fibrosis 230
                idiopathic pulmonary fibrosis 53
paths to the root