Tissue Disease Species symbol ID Platform Type Expression Target Pathway Method Drug Function PMID Title Year heart endomyocardial_fibrosis homo_sapiens RASSF1-A 11186 Gene mRNA down-regulation NA RAS SIGNALING PATHWAY NA no DNAMT3A likely plays an essential role in rassf1a mediated upregulation of erk1/2 in rat cardiac fibrosis. DNMT3A and Rassf1a may serve as a new mechanism for cardiac fibrosis. 24945829 DNMT3A silencing RASSF1A promotes cardiac fibrosis through upregulation of ERK1/2 2014 heart endomyocardial_fibrosis homo_sapiens RASAL1 8437 Gene mRNA methylation NA TGF-BETA SIGNALING PATHWAY qPCR; enzyme-linked immunosorbent assay etc. no "Hif1 alfa and transforming growth factor (TGF) / smad signaling pathway regulate hypoxia induced endothelial-to-mesenchymal transition (EndMT). through dnmt3a mediated rasal1 promoter hypermethylation and direct snail induction, and participate in the process of myocardial fibrosis." 27012941 Hypoxia-induced endothelial-mesenchymal transition is associated with RASAL1 promoter hypermethylation in human coronary endothelial cells. 2016 heart heart_failure homo_sapiens BMP7 655 Gene mRNA hyper-methylation NA NOTCH SIGNALING PATHWAY PCR; dual-luciferase reporter assay etc. no Highly methylated bmp-7 can block the end epithelial-mesenchymal transition (EMT) induced by TGF-beta and reduce fibrosis by regulating the activity of ve cadherin promoter. 25587097 Endocardial fibroelastosis is caused by aberrant endothelial to mesenchymal transition 2015 heart cardiomegaly homo_sapiens IGF-IIR 25151 Gene mRNA histone acetylation NA NA NA no Histone acetylation plays a critical role in IGF-iir up-regulation during pathological cardiac diseases and might provide a targeting gene in transcriptional therapies for the failing heart. 21412773 Histone acetylation is essential for ANG-II-induced IGF-IIR gene expression in H9c2 cardiomyoblast cells and pathologically hypertensive rat heart. 2013 heart atrial_fibrillation homo_sapiens WWP-1 11059 Gene mRNA up-regulation WWP-1 TGF-BETA SIGNALING PATHWAY PCR; MTT ASSAY etc. no miR-21 inhibits cardiac fibroblasts proliferation by inactivating the TGF-beta1/smad2 signaling pathway via up-regulation of WWP1. 28495464 MicroRNA-21 via Dysregulation of WW Domain-Containing Protein 1 Regulate Atrial Fibrosis in Atrial Fibrillation 2017 heart heart_failure homo_sapiens MECP2 4204 Gene mRNA methylation NA NA CHIP; PCR etc. no miR-212/132 was upregulated after transverse aortic constriction or on activation of alfa1- and beta1-adrenoceptors and miR-212/132 led to repression of methyl-CpG-binding protein 2 (MeCP2). 26195221 Adrenergic Repression of the Epigenetic Reader MeCP2 Facilitates Cardiac Adaptation in Chronic Heart Failure. 2015 heart myocardial_infarction homo_sapiens PFN2 5217 Gene mRNA up-regulation MIR-378;GRB2 NA dual-luciferase reporter assay no "PCFL, and the mechanism involves the direct interaction of PCFL with miR-378, which in turn relieves the inhibition effect of miR-378 on GRB2 and promotes cardiac fibrosis." 31220469 LncRNA PCFL promotes cardiac fibrosis via miR-378/GRB2 pathway following myocardial infarction 2019 heart endomyocardial_fibrosis homo_sapiens PFN2 5217 Gene mRNA up-regulation PTAFR NA immunofluorescence; qRT-PCR no Pfl/ptafr/let-7d-dependent gene regulatory mechanism proposed by the authors manifests the hypothesis of competing endogenous rnas to cardiac fibrosis. 29463987 LET's sponge: How the lncRNA PFL promotes cardiac fibrosis/LncRNA PFL contributes to cardiac fibrosis by acting as a competing endogenous RNA of let-7d 2018 heart diabetic_cardiomyopathy homo_sapiens PRPF31 26121 Gene mRNA down-regulation ZEB1 NA RT-PCR; etc. yes Rg1 inhibited high-glucose (HG)-induced mesenchymal activation and fibrosis via regulating miR-2113/rp11-982m15.8/Zeb1 pathway. 29654764 Rg1 inhibits high glucose-induced mesenchymal activation and fibrosis via regulating miR-2113/RP11-982M15.8/Zeb1 pathway 2018 heart endomyocardial_fibrosis homo_sapiens RASAL1 8437 Gene mRNA methylation NA NA CHIP; dual-luciferase reporter assay etc. no Transcriptional suppression of rasal1 through aberrant promoter methylation contributes to endothelial-to-mesenchymal transition (EndMT) and ultimately to progression of cardiac fibrosis. 25616414 Epigenetic balance of aberrant Rasal1 promoter methylation and hydroxymethylation regulates cardiacfibrosis. 2015 heart cardiomegaly homo_sapiens MYH7B 57644 Gene mRNA up-regulation NA CALCIUM SIGNALING PATHWAY Echocardiography no NA 32207065 MYH7B variants cause hypertrophic cardiomyopathy by activating the CaMK-signaling pathway 2020 kidney diabetic_nephropathy homo_sapiens PAQR9 344838 Gene mRNA up-regulation NRF2;HO-1 NF-KAPPA B SIGNALING PATHWAY qPCR; dual-luciferase reporter assay no "BLNC1 can affect inflammation, oxidative stress and renal fibrosis by NRF2/HO-1 and NF-KB pathways in diabetic nephropathies(dn)." 31632538 LncRNA Blnc1 expression and its effect on renal fibrosis in diabetic nephropathy 2019 kidney diabetic_nephropathy homo_sapiens ZEB1 6935 Gene mRNA down-regulation BMP7 TGF-BETA SIGNALING PATHWAY qPCR; dual-luciferase reporter assay no LncRNA ZEB1-AS1 inhibited high glucose-induced epithelial-mesenchymal transition (EMT) and fibrogenesis via regulating miR-216a-5p/bmp7 axis in diabetic nephropathy. 32294702 LncRNA ZEB1-AS1 inhibits high glucose-induced EMT and fibrogenesis by regulating the miR-216a-5p/BMP7 axis in diabetic nephropathy 2020 liver liver_cirrhosis homo_sapiens HOTAIR 100124700 Gene mRNA dna methylation PTEN ERK; PI3K-AKT SIGNALING PATHWAY RT-PCR; dual-lucimmunofluorescenceerase reporter assay etc. no A histone deacetylase-4-dependent mechanism underlies the epigenetic silencing of mmp genes during tissue fibrogenesis. 28129115 HOTAIR Epigenetically Modulates PTEN Expression via MicroRNA-29b: A Novel Mechanism in Regulation of Liver Fibrosis 2017 liver hepatitis homo_sapiens IGF2 3481 Gene mRNA igf2 methylation IGF2 NA methylation analysis; dna extraction; bisulfite treatment of dna etc. no Angiogenic factor with g patch and fha domains 1 (aggf1) regulates liver fibrosis by modulating tgf-b signaling. 22902352 Insulin-like growth factor 2 gene methylation in peripheral blood mononuclear cells of patients with hepatitis C related cirrhosis or hepatocellular carcinoma 2012 liver liver_cirrhosis homo_sapiens ASH1L 55870 Gene mRNA histone methylation ASH1 NA qRT-PCR; xmiRNA microarray chip detection etc. no "Curcumin can up-regulate mir-29b expression, resulting in dnmt3b down-regulation in hscs and epigenetically-regulated pten involved in the suppression of activated hscs." 22488473 Histone methyltransferase ASH1 orchestrates fibrogenic gene transcription during myofibroblast transdifferentiation 2012 liver liver_cirrhosis homo_sapiens SIRT3 23410 Gene mRNA hyperacetylation of glycogen synthase kinase 3b (gsk3b) GSK3B TGF-BETA SIGNALING PATHWAY NA no "Ethanol caused dose and time-dependent increase in acetylation of histone h3 at lys9, but not at lys14 or lys18. Compared with hepatocytes the ac-h3-lys9 in hscs required longer ethanol exposure. Levels of me-h3-lys9 seemed to remain unaltered. Thus increase in ac-h3-lys9 represents a nuclear-chromatin modification event in hscs exposed to ethanol." 26667039 SIRT3 Blocks Aging-Associated Tissue Fibrosis in Mice by Deacetylating and Activating Glycogen Synthase Kinase 3B 2015 liver liver_cirrhosis homo_sapiens SOCS1 8651 Gene mRNA socs1 methylation SOCS1 TGF-BETA SIGNALING PATHWAY RT-PCR; immunohistostaining etc. no Genetic and pharmacologic disruptions of mecp2 or ezh2 reduced the fibrogenic characteristics of myofibroblasts and attenuated fibrogenesis. 15197228 SOCS1 is a suppressor of liver fibrosis and hepatitis-induced carcinogenesis 2004 liver liver_cirrhosis homo_sapiens CFTR 1080 Gene mRNA histone deacetylase CFTR WNT SIGNALING PATHWAY miRNA microarray chip detection analysis; qmiRNA microarray chip detection; immunoblotting etc. no Hdac2 may play a pivotal role in hscs activation and liver fibrosis while deregulation of hdacs may serve as a novel mechanism underlying liver fibrosis. 17848139 The epigenetic signature of CFTR expression is co-ordinated via chromatin acetylation through a complex intronic element 2007 liver liver_cirrhosis homo_sapiens H2AC20 8338 Gene mRNA dna methylation H2A NA in vivo electroporation; immunostaining; quantimmunofluorescenceication no "Reveals a new cross histone crosstalk, including h2a ubiquitin change control of h3k4 methylation and methylation, lead to the regulation of transcription initiation." 18172164 Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation 2008 liver non-alcoholic_fatty_liver_disease homo_sapiens PPP1CC 5501 Gene mRNA phosphatase pp1c PP1C PHOSPHO-EIF-2A KINASE-MEDIATED STRESS immunoprecipitation; immunoblot etc. no Sirt2;Erk;C-myc axis in promoting hepatic fibrogenesis. Inhibition of the sirt2;Erk;C-myc axis represents a novel strategy to prevent and to potentially treat liver fibrosis and cirrhosis. 25888330 "Hepatocyte Nicotinamide Adenine Dinucleotide Phosphate Reduced Oxidase 4 Regulates Stress Signaling, Fibrosis, and Insulin Sensitivity During Development of Steatohepatitis in Mice" 2015 liver liver_cirrhosis homo_sapiens SIRT2 22933 Gene mRNA histone deacetylase SIRT2 NA qRT-PCR; immunofluorescence; etc. no "Sumoylation of nrf2 and mafg enhances heterodimerization and increases gclc expression, which keeps hscs in a quiescent state. Antifibrotic agents require activation of gclc to fully exert their protective effect." 27125275 Inhibition of SIRT2 suppresses hepatic fibrosis 2016 liver liver_cirrhosis homo_sapiens CREB1 1385 Gene mRNA creb-1 phosphorylation NA TGF-BETA SIGNALING PATHWAY RT-PCR; dual-lucimmunofluorescenceerase reporter assay etc. no "The increase in opn induces hmgb1, which acts as a downstream alarmin driving collagen-i synthesis in hscs." 27840939 Post translational modification of creb-1 decreases collagen I expression by inhibiting the TGF B1 signaling pathway in rat hepatic stellate cells 2016 lung Hypertension_Pulmonary homo_sapiens EDN1 1906 Gene mRNA down-regulation ET-1; TGFBR1 NA qRT-PCR; ELISA etc. no "35 MicroRNAs were differentially expressed in CTEPH patients, among which, a signature of 17 microRNAs was shown to be related to the disease pathogenesis by in silico analysis. Let-7b, one of the down-regulated anti-oncogenic microRNAs in the signature, was validated to decrease in CTEPH patients. ET-1 and TGFBR1 were direct targets of let-7b. Altering let-7b level influenced ET-1 and TGFBR1 expression in pulmonary arterial endothelial cells (PAECs) as well as the migration of PAECs and pulmonary arterial smooth muscle cells (PASMCs). CTEPH patients had aberrant microRNA signature which might provide some clue for pathogenesis study and biomarker screening. Reduced let-7b might be involved in the pathogenesis of CTEPH by affecting ET-1 expression and the function of PAECs and PASMCs." 24978044 Differentially Expressed Plasma MicroRNAs and the Potential Regulatory Function of Let-7b in Chronic Thromboembolic Pulmonary Hypertension 2014 lung Hypertension_Pulmonary homo_sapiens TGFBR1 7046 Gene mRNA down-regulation ET-1; TGFBR1 NA qRT-PCR; ELISA etc. no "35 MicroRNAs were differentially expressed in CTEPH patients, among which, a signature of 17 microRNAs was shown to be related to the disease pathogenesis by in silico analysis. Let-7b, one of the down-regulated anti-oncogenic microRNAs in the signature, was validated to decrease in CTEPH patients. ET-1 and TGFBR1 were direct targets of let-7b. Altering let-7b level influenced ET-1 and TGFBR1 expression in pulmonary arterial endothelial cells (PAECs) as well as the migration of PAECs and pulmonary arterial smooth muscle cells (PASMCs). CTEPH patients had aberrant microRNA signature which might provide some clue for pathogenesis study and biomarker screening. Reduced let-7b might be involved in the pathogenesis of CTEPH by affecting ET-1 expression and the function of PAECs and PASMCs." 24978044 Differentially Expressed Plasma MicroRNAs and the Potential Regulatory Function of Let-7b in Chronic Thromboembolic Pulmonary Hypertension 2014 lung Hypertension_Pulmonary homo_sapiens FGA 2243 Gene mRNA dysregulation NA NA Dual-luciferase reporter assay; etc. no "A deletion/insertion (Del/Ins) polymorphism of 28 base pairs (bp) in the 3' untranslated region (UTR) of fibrinogen alpha gene (FGA) was associated with thromboembolic diseases. The expression of FGA was regulated by miR-759 through its interaction at the polymorphic 3'UTR sequence, which was associated with the susceptibility to CTEPH. And the effect of miR-759 was stronger on the Ins allele than on the Del allele." 20677013 Susceptibility to chronic thromboembolic pulmonary hypertension may be conferred by miR-759 via its targeted interaction with polymorphic fibrinogen alpha gene 2010 lung idiopathic_pulmonary_fibrosis homo_sapiens SERPINE1 5054 Gene mRNA up-regulation NA NA AEC purification; A549 cell wounding assay; Bleomycin exposure etc. no Accentuated impairment of plasminogen activation through PAI-1 overexpression leads to exuberant fibrosis after lung injury. 15308506 Plasminogen activator inhibitor-1 impairs alveolar epithelial repair by binding to vitronectin 2004 lung pulmonary_arterial_hypertension homo_sapiens BMP2 650 Gene mRNA up-regulation NA NA PKC activity; qRT-PCR; etc. no "An imbalance of bone morphogenetic protein-2/endothelin-1 systems may contribute to the progression of lung fibrosis, and to vascular remodeling in PAH." 21659661 Opposing effects of bone morphogenetic protein-2 and endothelin-1 on lung fibroblast chloride currents 2011 lung idiopathic_pulmonary_fibrosis homo_sapiens COL1A2 1278 Gene mRNA up-regulation NA NA qRT-PCR; ELISA; etc. no "As expected, COL1A2, MMP1, and MMP7 were significantly higher and AGER was significantly lower in IPF and IPF-AEx compared with control samples, but there was no significant difference in their expression between IPF and IPF-AEx." 19363140 Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis 2009 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP1 4312 Gene mRNA up-regulation NA NA qRT-PCR; ELISA; etc. no "As expected, COL1A2, MMP1, and MMP7 were significantly higher and AGER was significantly lower in IPF and IPF-AEx compared with control samples, but there was no significant difference in their expression between IPF and IPF-AEx." 19363140 Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis 2009 lung idiopathic_pulmonary_fibrosis homo_sapiens AGER 177 Gene mRNA down-regulation NA NA qRT-PCR; ELISA; etc. no "As expected, COL1A2, MMP1, and MMP7 were significantly higher and AGER was significantly lower in IPF and IPF-AEx compared with control samples, but there was no significant difference in their expression between IPF and IPF-AEx." 19363140 Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis 2009 lung idiopathic_pulmonary_fibrosis homo_sapiens DEFA4 1669 Gene mRNA up-regulation NA NA Pulmonary function testing; Quality characterization; Gene ontology and functional network analysis etc. no "Between the mild and severe IPF cohort , and between normal and severe disease, there is up-regulation of several other host defense genes including defensin A4 (DEFA4), cathelicidin antimicrobial peptide (CAMP), cathespin G (CTSG), and down-regulation of immunoglobulin heavy chain constant mu (IGHM)." 22761659 The peripheral blood transcriptome identifies the presence and extent of disease in idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens CAMP 820 Gene mRNA up-regulation NA NA Pulmonary function testing; Quality characterization; Gene ontology and functional network analysis etc. no "Between the mild and severe IPF cohort , and between normal and severe disease, there is up-regulation of several other host defense genes including defensin A4 (DEFA4), cathelicidin antimicrobial peptide (CAMP), cathespin G (CTSG), and down-regulation of immunoglobulin heavy chain constant mu (IGHM)." 22761659 The peripheral blood transcriptome identifies the presence and extent of disease in idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens CTSG 1511 Gene mRNA up-regulation NA NA Pulmonary function testing; Quality characterization; Gene ontology and functional network analysis etc. no "Between the mild and severe IPF cohort , and between normal and severe disease, there is up-regulation of several other host defense genes including defensin A4 (DEFA4), cathelicidin antimicrobial peptide (CAMP), cathespin G (CTSG), and down-regulation of immunoglobulin heavy chain constant mu (IGHM)." 22761659 The peripheral blood transcriptome identifies the presence and extent of disease in idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens CCL8 6355 Gene mRNA up-regulation NA CYTOKINE-CYTOKINE RECEPTOR INTERACTION signaling pathway qRT-PCR; ELISA; Immunofluorescence etc. no CCL8 is a candidate molecule for the differential diagnosis and prediction of survival. 28057004 Gene profile of fibroblasts identify relation of CCL8 with idiopathic pulmonary fibrosis 2017 lung idiopathic_pulmonary_fibrosis homo_sapiens SFTPA1 653509 Gene mRNA up-regulation NA NA "Change in FVC and DLco, and definition of deterioration; Changes in SP-A, SP-D, and KL-6; Statistical analysis etc." no Changes in serum SP-A reflected the outcomes of anti-fibrotic drug therapy. Serum SP-A has a potential as a biomarker of therapeutic outcomes of anti-fibrotic drugs. 32005219 Surfactant protein A as a biomarker of outcomes of anti-fibrotic drug therapy in patients with idiopathic pulmonary fibrosis 2020 lung idiopathic_pulmonary_fibrosis homo_sapiens DNMT1 1786 Gene mRNA dysregulation NA NA qRT-PCR; Examination of DNA methylation patterns; Dual-luciferase reporter assay etc. no "Compared with control samples, miR-17~92 expression was reduced in lung biopsies and lung fibroblasts from patients with IPF, whereas DNMT-1 expression and methylation of the miR-17~92 promoter was increased. Several miRNAs from the miR-17~92 cluster targeted DNMT-1 expression resulting in a negative feedback loop. Similarly, miR-17~92 expression was reduced in the lungs of bleomycin-treated mice. Treatment with 5'-aza-2'-deoxycytidine in a murine bleomycin-induced pulmonary fibrosis model reduced fibrotic gene and DNMT-1 expression, enhanced miR-17~92 cluster expression, and attenuated pulmonary fibrosis." 23306545 Epigenetic regulation of miR-17~92 contributes to the pathogenesis of pulmonary fibrosis 2013 lung pulmonary_hypertension homo_sapiens CDKN1A 1026 Gene mRNA dna methylation NA NA BrdU incorporation assay; qRT-PCR; etc. no "Compared with controls, in high-altitude long-term hypoxia(LTH)fetus pulmonary arteries,global histone 4 acetylation and DNA methylation levels are reduced, accompanied by the loss of the cyclin-dependent kinase inhibitor p21. Treatment of LTH fetal PASMCs with histone deacetylase (HDAC) inhibitor trichostatin A decreased their proliferation rate, PDGF-induced cell migration, ERK1/2 activation and modulated global DNA methylation. Epigenetic alterations (reduced histone acetylation and DNA methylation) caused by chronic hypoxia leads to fetal PASMC proliferation and vessel remodeling associated with vascular proliferative disease and that this process is regulated by p21." 23043075 Pulmonary artery smooth muscle cell proliferation and migration in fetal lambs acclimatized to high-altitude long-term hypoxia: role of histone acetylation 2012 lung pulmonary_hypertension homo_sapiens CDKN1A 1026 Gene mRNA histone acetylation NA NA BrdU incorporation assay; qRT-PCR; etc. no "Compared with controls, in high-altitude long-term hypoxia(LTH)fetus pulmonary arteries,global histone 4 acetylation and DNA methylation levels are reduced, accompanied by the loss of the cyclin-dependent kinase inhibitor p21. Treatment of LTH fetal PASMCs with histone deacetylase (HDAC) inhibitor trichostatin A decreased their proliferation rate, PDGF-induced cell migration, ERK1/2 activation and modulated global DNA methylation. Epigenetic alterations (reduced histone acetylation and DNA methylation) caused by chronic hypoxia leads to fetal PASMC proliferation and vessel remodeling associated with vascular proliferative disease and that this process is regulated by p21." 23043075 Pulmonary artery smooth muscle cell proliferation and migration in fetal lambs acclimatized to high-altitude long-term hypoxia: role of histone acetylation 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens DHX58 79132 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens IDO1 3602 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens IFI44 10561 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens CASP1 834 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens PSMB9 5698 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens PSMB10 5699 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens SLC15A3 51296 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens UBA7 7318 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens ASPA 443 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens SLC12A7 10723 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens TAP1 6890 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens IFI35 3430 Gene mRNA down-regulation NA NA Data compilation; Statistical analysis etc. no "Consistent with repression of processes involved in the immune/inflammatory response, the downregulated list was enriched with genes bearing binding sites for the Interferon Response Factor (IRF) transcription factor (11 genes out of 158 in the annotation: DHX58, IDO1, IFI44, CASP1, PSMB9, PSMB10, SLC15A3, UBA7, ASPA, SLC12A7, TAP1, p = 4.2E-6) And the Interferon Consensus Sequence Binding Protein (ICSBP) transcription factor (9 genes out of 203 in the annotation : IDO1, IFI44, PSMB9, SLC15A3, IFI35, UBA7, ASPA, SLC12A7, TAP1; P = 3.2E-3)." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens CCN2 1490 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "CTGF, a member of the CCN protein family, is a highly potent extracellular matrix-associated mitogen. In vitro, CTGF induces collagen-1 expression in lung fibroblasts [20]. In vivo, overexpression of CTGF in fibroblasts drives fibrogenesis in multiple organs including the lung [21]. CTGF is overexpressed in IPF, with expression localized to alveolar epithelial cells and fibroblasts [22]. Consistent for a role of CTGF in IPF, a recent open-label uncontrolled study suggested that a monoclonal antibody targeting CTGF, FG-3019, may be beneficial in a subset of IPF patients in terms of lung function decline and imaging-assessed fibrotic changes [23]." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens CTHRC1 115908 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no "Cthrc1 is expressed by fibroblasts, is involved in vascular remodeling, and decreases collagen matrix deposition . Cthrc1 is a downstream target of bone morphogenic protein-SMAD signaling, inhibits TGF-beta expression in neointimal lesion formation, and acts as a Wnt cofactor, possibly contributing to the promotion of cell motility. " 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens PTGS2 5743 Gene mRNA down-regulation NA NA qRT-PCR; Statistical analysis etc. no "Cyclooxygenase-2, a key regulatory enzyme in the synthesis of the antifibrotic agent prostaglandin E2, is downregulated in lung tissue from patients with idiopathic pulmonary fibrosis." 21319594 A haplotype of cyclooxygenase-2 gene is associated with idiopathic pulmonary fibrosis 2010 lung idiopathic_pulmonary_fibrosis homo_sapiens TCIM 56892 Gene mRNA dna hypermethylation NA NA qRT-PCR; Immunohistochemistry; etc. no "Decreased capacity of fibrotic lung fibroblasts to up-regulate COX-2 expression and COX-2-derived PGE2 synthesis is due to an indirect epigenetic mechanism involving hypermethylation of the transcriptional regulator, c8orf4." 26744410 Epigenetic regulation of cyclooxygenase-2 by methylation of c8orf4 in pulmonary fibrosis 2016 lung cystic_fibrosis homo_sapiens HMOX1 3162 Gene mRNA dna methylation NA NA DNA methylation correlations in CF cells; DNA methylation analysis in NEC; DNA methylation at HMOX1 was not associated with nearby polymorphisms etc. no DNA methylation levels are altered in nasal epithelial and blood cell samples from CF patients. Analysis of CFTR and 13 lung disease modifier genes shows DNA methylation changes of small magnitude: some of them are a consequence of the disease; Other changes may result in small expression variations that collectively modulate the lung disease severity. Three genes were differentially methylated in CF patients compared with controls and/or in groups of pulmonary severity: HMOX1 and GSTM3 in nasal epithelial samples; HMOX1 and EDNRA in blood samples. The association between pulmonary severity and DNA methylation at EDNRA was confirmed in blood samples from an independent set of CF patients. 28289476 DNA methylation at modifier genes of lung disease severity is altered in cystic fibrosis 2017 lung cystic_fibrosis homo_sapiens EDNRA 1909 Gene mRNA dna methylation NA NA DNA methylation correlations in CF cells; DNA methylation analysis in NEC; DNA methylation at HMOX1 was not associated with nearby polymorphisms etc. no DNA methylation levels are altered in nasal epithelial and blood cell samples from CF patients. Analysis of CFTR and 13 lung disease modifier genes shows DNA methylation changes of small magnitude: some of them are a consequence of the disease; Other changes may result in small expression variations that collectively modulate the lung disease severity. Three genes were differentially methylated in CF patients compared with controls and/or in groups of pulmonary severity: HMOX1 and GSTM3 in nasal epithelial samples; HMOX1 and EDNRA in blood samples. The association between pulmonary severity and DNA methylation at EDNRA was confirmed in blood samples from an independent set of CF patients. 28289476 DNA methylation at modifier genes of lung disease severity is altered in cystic fibrosis 2017 lung cystic_fibrosis homo_sapiens GSTM3 2947 Gene mRNA dna methylation NA NA DNA methylation correlations in CF cells; DNA methylation analysis in NEC; DNA methylation at HMOX1 was not associated with nearby polymorphisms etc. no DNA methylation levels are altered in nasal epithelial and blood cell samples from CF patients. Analysis of CFTR and 13 lung disease modifier genes shows DNA methylation changes of small magnitude: some of them are a consequence of the disease; Other changes may result in small expression variations that collectively modulate the lung disease severity. Three genes were differentially methylated in CF patients compared with controls and/or in groups of pulmonary severity: HMOX1 and GSTM3 in nasal epithelial samples; HMOX1 and EDNRA in blood samples. The association between pulmonary severity and DNA methylation at EDNRA was confirmed in blood samples from an independent set of CF patients. 28289476 DNA methylation at modifier genes of lung disease severity is altered in cystic fibrosis 2017 lung idiopathic_pulmonary_fibrosis homo_sapiens ABAT 18 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens FAM168B 130074 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens PPRC1 23082 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens DVL3 1857 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens ZMIZ1 57178 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens SLC38A1 81539 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens XYLT1 64131 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens ARL4A 10124 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens ADO 84890 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens FAM168A 23201 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens PLEKHA3 65977 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens AUTS2 26053 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "Enrichment in genes putatively regulated by the microRNA miR-153 was observed among upregulated transcripts (13 genes out of 153 in the annotation: ABAT, FAM168B, PPRC1, DVL3, ZMIZ1, MFAPL3, SLC38A1, XYLT1, ARL4A, ADO, FAM168A, PLEKHA3, AUTS2, p = 1.2E-2). Functional annotation analysis did not identify enrichment of Gene Ontology, pathway, functional class nor transcription factor binding site categories among transcripts upregulated in IPF fibroblasts." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung pulmonary_arterial_hypertension homo_sapiens CCL24 6369 Gene mRNA up-regulation NA NA Biochemical staining; Immunostaining; ELISA etc. no Eotaxin-2/CCL24 but not eotaxin-3/CCL26 stimulated human lung fibroblast proliferation and collagen synthesis. 20143648 Eotaxin-2/CCL24 and eotaxin-3/CCL26 exert differential profibrogenic effects on human lung fibroblasts 2010 lung pulmonary_arterial_hypertension homo_sapiens CCL26 10344 Gene mRNA up-regulation NA NA Biochemical staining; Immunostaining; ELISA etc. no Eotaxin-3/CCL26 but not eotaxin-2/CCL24 promoted fibroblast migration. 20143648 Eotaxin-2/CCL24 and eotaxin-3/CCL26 exert differential profibrogenic effects on human lung fibroblasts 2010 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL10 3627 Gene mRNA histone modification NA NA qRT-PCR; ELISA; etc. no Epigenetic dysregulation involving interactions between histone deacetylation and hypermethylation is responsible for targeted repression of IP-10 and potentially other antifibrotic genes in fibrotic lung disease and that this is amenable to therapeutic targeting. 20404089 Repression of IP-10 by interactions between histone deacetylation and hypermethylation in idiopathic pulmonary fibrosis 2010 lung pulmonary_hypertension homo_sapiens SOD3 6649 Gene mRNA histone acetylation NA JAK2/STAT3 signaling pathway; P44/42 ERK 1/2 signaling pathway ROS Measurement; Mtt assay; EC-SOD Immunoprecipitation etc. no "Exposure of HPAECs to scriptaid, N[4 [(hydroxyamino)carbonyl] phenyl]-a-(1-methylethyl)-benzeneacetamide, and trichostatin A for 24 hours induced expression of extracellular superoxide dismutase (EC-SOD), whereas expression of the prooxidant gene NADPH oxidase 4 was decreased. Induction of EC-SOD expression was attenuated by the Janus kinase 2 protein kinase inhibitor AG490 and by silencing Janus kinase 2 expression. Augmentation of EC-SOD expression using scriptaid was associated with increased histone H3 (Lys27) acetylation and H3 (Lys4) trimethylation at the gene promoter." 25749103 Regulation of Oxidative Stress in Pulmonary Artery Endothelium Modulation of Extracellular Superoxide Dismutase and NOX4 Expression Using Histone Deacetylase Class I Inhibitors 2015 lung pulmonary_hypertension homo_sapiens NOX4 50507 Gene mRNA histone acetylation NA JAK2/STAT3 signaling pathway; P44/42 ERK 1/2 signaling pathway ROS Measurement; Mtt assay; EC-SOD Immunoprecipitation etc. no "Exposure of HPAECs to scriptaid, N[4 [(hydroxyamino)carbonyl] phenyl]-a-(1-methylethyl)-benzeneacetamide, and trichostatin A for 24 hours induced expression of extracellular superoxide dismutase (EC-SOD), whereas expression of the prooxidant gene NADPH oxidase 4 was decreased. Induction of EC-SOD expression was attenuated by the Janus kinase 2 protein kinase inhibitor AG490 and by silencing Janus kinase 2 expression. Augmentation of EC-SOD expression using scriptaid was associated with increased histone H3 (Lys27) acetylation and H3 (Lys4) trimethylation at the gene promoter." 25749103 Regulation of Oxidative Stress in Pulmonary Artery Endothelium Modulation of Extracellular Superoxide Dismutase and NOX4 Expression Using Histone Deacetylase Class I Inhibitors 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens SMAD4 4089 Gene mRNA promoter hypermethylation NA NA qRT-PCR; PCR-SSCP etc. no Expression levels of Smad4 were significantly lower in tumors from lung cancer/IPF patients than in those from lung cancer patients without IPF or in lung cancer cell lines. The loss of the growth inhibitory response to TGF-B signaling may be crucial in pulmonary carcinogensis or in the progression of lung cancer in IPF patients in whom TGF-B is overexpressed; Hypermethylation of the Smad4 promoter region may be one mechanism by which this occurs. 21475793 Reduced transcription of the Smad4 gene during pulmonary carcinogenesis in idiopathicpulmonary fibrosis 2009 lung idiopathic_pulmonary_fibrosis homo_sapiens PTGS2 5743 Gene mRNA histone acetylation NA NA HDAC activity assay; ChIp assay; Reporter gene assay etc. no "HDAC inhibitors and the overexpression of HATs restored cytokine-induced COX-2 mRNA and protein expression in F-IPF. The results demonstrate that epigenetic abnormality in the form of histone hypoacetylation is responsible for diminished COX-2 expression in IPF. Diminished cyclooxygenase 2 (COX-2) expression in fibroblasts, with a resultant defect in the production of the antifibrotic mediator prostaglandin E(2), promote pathogenesis of idiopathic pulmonary fibrosis (IPF)." 19487460 Defective histone acetylation is responsible for the diminished expression of cyclooxygenase 2 in idiopathic pulmonary fibrosis 2009 lung Familial_Primary_Pulmonary_Hypertension homo_sapiens SMAD9 4093 Gene mRNA dysregulation NA NA etc. no "Heritable pulmonary arterial hypertension (HPAH) associated BMPR2 and SMAD9 mutation completely abrogated noncanonical Smad-mediated microRNA (miR) processing, leading to miR-21 downregulation, contributing to vascular cell proliferation." 21920918 Altered MicroRNA processing in heritable pulmonary arterial hypertension: an important role for Smad-8 2011 lung Familial_Primary_Pulmonary_Hypertension homo_sapiens BMPR2 659 Gene mRNA dysregulation NA NA etc. no "Heritable pulmonary arterial hypertension (HPAH) associated BMPR2 and SMAD9 mutation completely abrogated noncanonical Smad-mediated microRNA (miR) processing, leading to miR-21 downregulation, contributing to vascular cell proliferation." 21920918 Altered MicroRNA processing in heritable pulmonary arterial hypertension: an important role for Smad-8 2011 lung Idiopathic_Pulmonary_Arterial_Hypertension homo_sapiens SOD3 6649 Gene mRNA histone deacetylation NA NA qRT-PCR; SOD Activity etc. no "Histone deacetylation, specifically via class I HDAC3, decreases SOD3 expression in PASMC and HDAC inhibitors may protect IPAH in part by increasing PASMC SOD3 expression." 27233998 Histone deacetylation contributes to low extracellular superoxide dismutase expression in human idiopathic pulmonary arterial hypertension 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens TLR9 54106 Gene mRNA dna hypomethylation NA NA qRT-PCR; etc. no "Hypomethylated CpG DNA drives the rapid progression of fibrotic lung disease through the differentiation of pulmonary fibroblasts into myofibroblasts through a TLR9-dependent mechanism; Toll-like receptor 9 (TLR9)-dependent macroautophagy drive the loss of Argonaute (AGO)1 and AGO2, leading to aberrant micro RNA processing, thereby promoting the rapid progression of IPF." 22802293 Epigenetic mechanisms through which Toll-like receptor-9 drives idiopathic pulmonary fibrosis progression 2012 lung pulmonary_hypertension homo_sapiens DDAH1 23576 Gene mRNA up-regulation DDAH1 NA qRT-PCR; Dual-luciferase reporter assay etc. no "Hypoxia inhibited DDAH1 and DDAH2 expression and increased ADMA levels in cultured human pulmonary endothelial cells. In contrast, in human pulmonary smooth muscle cells, only DDAH2 was reduced whereas ADMA levels remained unchanged. Endothelium-specific down-regulation of DDAH1 by miR-21 in hypoxia induced endothelial dysfunction and was prevented by overexpression of DDAH1 and miR-21 blockade. DDAH1, but not DDAH2, mRNA levels were reduced, whereas miR-21 levels were elevated in lung tissues from patients with pulmonary arterial hypertension and mice with pulmonary hypertension exposed to 2 weeks of hypoxia." 24895913 MiR-21/DDAH1 pathway regulates pulmonary vascular responses to hypoxia 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens MNT 4335 Gene mRNA down-regulation MNT NA qRT-PCR; Immunohistochemistry etc. no "Hypoxia potently stimulates miR-210 expression via HIF-2a, and high miR-210 expression drives fibroblast proliferation by repressing the c-myc inhibitor, MNT." 24951777 MiR-210 promotes IPF fibroblast proliferation in response to hypoxia 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens EPAS1 2034 Gene mRNA down-regulation MNT NA qRT-PCR; Immunohistochemistry etc. no "Hypoxia potently stimulates miR-210 expression via HIF-2a, and high miR-210 expression drives fibroblast proliferation by repressing the c-myc inhibitor, MNT." 24951777 MiR-210 promotes IPF fibroblast proliferation in response to hypoxia 2014 lung pulmonary_fibrosis homo_sapiens TGFB1 7040 Gene mRNA histone hyperacetylation NA NF-kappaB signaling pathway; AP-1 signaling pathway qRT-PCR; ELISA etc. no "IL-1beta-stimulated transcription of TGF-Beta1 is temporally regulated by NF-kappaB and AP-1 and involves histone H3, H4 hyperacetylation at distinct promoter sites." 16365456 NF-kappaB and activator protein 1 response elements and the role of histone modifications in IL-1beta-induced TGF-Beta1 gene transcription 2006 lung cystic_fibrosis homo_sapiens CXCL8 3576 Gene mRNA up-regulation NA NA LD; Dual-luciferase reporter assay etc. no IL8 variants modify CF lung disease severity and have functional consequences. 18563170 Modulation of cystic fibrosis lung disease by variants in interleukin-9 2008 lung pulmonary_fibrosis homo_sapiens CDH1 999 Gene mRNA promoter hypermethylation NA NA Immunofluorescence; qRT-PCR etc. no "In bronchial epithelial cells, NiCl(2) induced EMT phenotype marker alterations such as up-regulation of fibronectin and down-regulation of E-cadherin. In addition, the potent antioxidant N-acetylcysteine blocked EMT and expression of HIF-1a induced by NiCl(2), whereas the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine restored the down-regulation of E-cadherin induced by NiCl(2). Promoter hypermethylation of E-cadherin was also induced by NiCl(2). Specifically, NiCl(2) induces down-regulation of E-cadherin by reactive oxygen species generation and promoter hypermethylation." 22648416 Nickel-induced epithelial-mesenchymal transition by reactive oxygen species generation and E-cadherin promoter hypermethylation 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens COL3A1 1281 Gene mRNA histone hyperacetylation NA NA qRT-PCR; Immunofluorescence; Immunohistochemistry etc. no "In fibrotic lung fibroblasts, reduced expression of COL3A1 by SAHA is with increased association of the repressive chromatin marker, H3K27Me3, and decreased association of the active chromatin marker, H3K9Ac. HDACi SAHA alters the chromatin associated with COL3A1, resulting in its decreased expression." 24084714 Histone Deacetylase Inhibition Downregulates Collagen 3A1 in Fibrotic Lung Fibroblasts 2013 lung idiopathic_pulmonary_fibrosis homo_sapiens WNT1 7471 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no "In IPF lung specimens, Wnt1, 7b, and 10b mRNA levels were markedly upregulated (log-fold change of 1.19+-0.43, 1.05+-0.43, And 1.58+-0.59, Respectively), whereas Wnt3a was significantly downregulated (log-fold change 1.93+-0.65)." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens WNT7B 7477 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no "In IPF lung specimens, Wnt1, 7b, and 10b mRNA levels were markedly upregulated (log-fold change of 1.19+-0.43, 1.05+-0.43, And 1.58+-0.59, Respectively), whereas Wnt3a was significantly downregulated (log-fold change 1.93+-0.65)." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens WNT10B 7480 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no "In IPF lung specimens, Wnt1, 7b, and 10b mRNA levels were markedly upregulated (log-fold change of 1.19+-0.43, 1.05+-0.43, And 1.58+-0.59, Respectively), whereas Wnt3a was significantly downregulated (log-fold change 1.93+-0.65)." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens WNT3A 89780 Gene mRNA down-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no "In IPF lung specimens, Wnt1, 7b, and 10b mRNA levels were markedly upregulated (log-fold change of 1.19+-0.43, 1.05+-0.43, And 1.58+-0.59, Respectively), whereas Wnt3a was significantly downregulated (log-fold change 1.93+-0.65)." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens THY1 7070 Gene mRNA promoter hypomethylation NA NA qRT-PCR; MSP; MSPISH etc. no "In IPF samples in which Thy-1 expression is absent, the Thy-1 promoter region is methylated, whereas in lung samples retaining Thy-1 expression, the promoter region is unmethylated. Treatment with DNA methyltransferase inhibitors restores Thy-1 expression in Thy-1(-) fibroblasts." 18556592 Thy-1 promoter hypermethylation: a novel epigenetic pathogenic mechanism in pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens NOX4 50507 Gene mRNA histone acetylation NA NA qRT-PCR; Immunoblot; Chromatin immunoprecipitation assay etc. no "In replicative senescent fibroblasts, the Nox4 gene is enriched with the activation histone mark, H4K16Ac, and inversely associated with the repressive histone mark, H4K20Me3, supporting an active transcriptional chromatin conformation. Silencing of the histone acetyltransferase Mof, which specifically acetylates H4K16, down-regulates Nox4 gene/protein expression." 25526894 Epigenetic mechanisms regulate NADPH oxidase-4 expression in cellular senescence 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens PLA2G2A 5320 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no "Ingenuity pathway analysis classification revealed enrichment of several pathways and functional groups among common up-regulated genes. For instance, PLA2G2A/Pla2 g2a, phospholipase A2, group VII (PLA2G7/Pla2 g7), prostaglandin E synthase (PTGES/Ptges), and glycerol-3-phosphate dehydrogenase 1 (GPD1/Gpd1) are eicosanoid signaling components, suggesting that the dysregulation of this particular pathway is well conserved between the animal model and IPF, a finding of significant interest considering the phenotype of prostaglandin synthase 2 knockout mice. " 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens PLA2G7 7941 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no "Ingenuity pathway analysis classification revealed enrichment of several pathways and functional groups among common up-regulated genes. For instance, PLA2G2A/Pla2 g2a, phospholipase A2, group VII (PLA2G7/Pla2 g7), prostaglandin E synthase (PTGES/Ptges), and glycerol-3-phosphate dehydrogenase 1 (GPD1/Gpd1) are eicosanoid signaling components, suggesting that the dysregulation of this particular pathway is well conserved between the animal model and IPF, a finding of significant interest considering the phenotype of prostaglandin synthase 2 knockout mice. " 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens PTGES 9536 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no "Ingenuity pathway analysis classification revealed enrichment of several pathways and functional groups among common up-regulated genes. For instance, PLA2G2A/Pla2 g2a, phospholipase A2, group VII (PLA2G7/Pla2 g7), prostaglandin E synthase (PTGES/Ptges), and glycerol-3-phosphate dehydrogenase 1 (GPD1/Gpd1) are eicosanoid signaling components, suggesting that the dysregulation of this particular pathway is well conserved between the animal model and IPF, a finding of significant interest considering the phenotype of prostaglandin synthase 2 knockout mice. " 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens GPD1 2819 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no "Ingenuity pathway analysis classification revealed enrichment of several pathways and functional groups among common up-regulated genes. For instance, PLA2G2A/Pla2 g2a, phospholipase A2, group VII (PLA2G7/Pla2 g7), prostaglandin E synthase (PTGES/Ptges), and glycerol-3-phosphate dehydrogenase 1 (GPD1/Gpd1) are eicosanoid signaling components, suggesting that the dysregulation of this particular pathway is well conserved between the animal model and IPF, a finding of significant interest considering the phenotype of prostaglandin synthase 2 knockout mice. " 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens CDKN2B 1030 Gene mRNA dna methylation NA NA DNA methylation analysis; qRT-PCR; Immunoblot etc. no "IPF fibroblasts exhibit global differences in DNA methylation that may contribute to the excessive fibroproliferation associated with this disease. DNA methylation differences in 3 genes (CDKN2B, CARD10, and MGMT) corresponded with differences in gene expression at the mRNA and protein level." 25215577 Lung fibroblasts from patients with idiopathic pulmonary fibrosis exhibit genome-wide differences in DNA methylation compared to fibroblasts from nonfibrotic lung 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens CARD10 29775 Gene mRNA dna methylation NA NA DNA methylation analysis; qRT-PCR; Immunoblot etc. no "IPF fibroblasts exhibit global differences in DNA methylation that may contribute to the excessive fibroproliferation associated with this disease. DNA methylation differences in 3 genes (CDKN2B, CARD10, and MGMT) corresponded with differences in gene expression at the mRNA and protein level." 25215577 Lung fibroblasts from patients with idiopathic pulmonary fibrosis exhibit genome-wide differences in DNA methylation compared to fibroblasts from nonfibrotic lung 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens MGMT 4255 Gene mRNA dna methylation NA NA DNA methylation analysis; qRT-PCR; Immunoblot etc. no "IPF fibroblasts exhibit global differences in DNA methylation that may contribute to the excessive fibroproliferation associated with this disease. DNA methylation differences in 3 genes (CDKN2B, CARD10, and MGMT) corresponded with differences in gene expression at the mRNA and protein level." 25215577 Lung fibroblasts from patients with idiopathic pulmonary fibrosis exhibit genome-wide differences in DNA methylation compared to fibroblasts from nonfibrotic lung 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens CDKN2A 1029 Gene mRNA dna hypermethylation NA NA Genomic DNA digestion and promoter amplification; qRT-PCR; etc. no "IPF fibroblasts have reduced expression of the proapoptotic p14(ARF) attributable to promoter hypermethylation, wand the p14(ARF)-hypermethylated IPF fibroblasts were significantly more resistant to staurosporine-and S-nitrosoglutathione-induced apoptosis compared with normal and nonmethylated IPF fibroblasts (P < 0.01) And showed reduced levels of p53." 22707614 Hypermethylation-mediated silencing of p14(ARF) in fibroblasts from idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens CLDN5 7122 Gene mRNA dna methylation NA NA MSP; qRT-PCR; etc. no "IPF samples demonstrated higher DNA methyltransferase expression without observed alterations in global DNA methylation. Among the genes whose DNA methylation status and RNA expression were both significantly altered, 16 genes were hypermethylated in DNA associated with decreased mRNA expression or vice versa.Changes in DNA methylation correspond to altered mRNA expression of a number of genes, some with known and others with previously uncharacterized roles in IPF, suggesting that DNA methylation is important in the pathogenesis of IPF." 22700861 Altered DNA methylation profile in idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens ZNF467 168544 Gene mRNA dna methylation NA NA MSP; qRT-PCR; etc. no "IPF samples demonstrated higher DNA methyltransferase expression without observed alterations in global DNA methylation. Among the genes whose DNA methylation status and RNA expression were both significantly altered, 16 genes were hypermethylated in DNA associated with decreased mRNA expression or vice versa.Changes in DNA methylation correspond to altered mRNA expression of a number of genes, some with known and others with previously uncharacterized roles in IPF, suggesting that DNA methylation is important in the pathogenesis of IPF." 22700861 Altered DNA methylation profile in idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens TP53INP1 94241 Gene mRNA dna methylation NA NA MSP; qRT-PCR; etc. no "IPF samples demonstrated higher DNA methyltransferase expression without observed alterations in global DNA methylation. Among the genes whose DNA methylation status and RNA expression were both significantly altered, 16 genes were hypermethylated in DNA associated with decreased mRNA expression or vice versa.Changes in DNA methylation correspond to altered mRNA expression of a number of genes, some with known and others with previously uncharacterized roles in IPF, suggesting that DNA methylation is important in the pathogenesis of IPF." 22700861 Altered DNA methylation profile in idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens DDAH1 23576 Gene mRNA dna methylation NA NA MSP; qRT-PCR; etc. no "IPF samples demonstrated higher DNA methyltransferase expression without observed alterations in global DNA methylation. Among the genes whose DNA methylation status and RNA expression were both significantly altered, 16 genes were hypermethylated in DNA associated with decreased mRNA expression or vice versa.Changes in DNA methylation correspond to altered mRNA expression of a number of genes, some with known and others with previously uncharacterized roles in IPF, suggesting that DNA methylation is important in the pathogenesis of IPF." 22700861 Altered DNA methylation profile in idiopathic pulmonary fibrosis 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens KCNJ2 3759 Gene mRNA up-regulation NA NA qRT-PCR; ELISA; Statistical analysis etc. no KCNJ2 may be an indicator of the development of IPF and a surrogate marker for IPF differential diagnosis. 32184906 Upregulation of Potassium Voltage-Gated Channel Subfamily J Member 2 Levels in the Lungs of Patients with Idiopathic Pulmonary Fibrosis 2020 lung idiopathic_pulmonary_fibrosis homo_sapiens FGF7 2252 Gene mRNA up-regulation NA ERK-1 AND P38 MAP KINASE signaling pathway "Quantitative Analysis of KGF, JunB, and c-Jun mRNA; Statistical Analysis etc." no Keratinocyte growth factor (KGF) is secreted by fibroblasts and protects from pulmonary fibrosis in animal models. 15677771 Keratinocyte growth factor expression by fibroblasts in pulmonary fibrosis: poor response to interleukin-1beta 2005 lung idiopathic_pulmonary_fibrosis homo_sapiens LEF1 51176 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no Lef1 was significantly upregulated in IPF (log-fold change 0.85+-0.34). 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens PTGS2 5743 Gene mRNA histone hypermethylation NA NA qRT-PCR; ELISA etc. no "Marked increases in H3K9me3, H3K27me3, and DNA methylation, together with their respective modifying enzymes G9a, EZH2, and DNA methyltransferases (Dnmts) and respective binding proteins heterochromatin protein 1 (HP1), polycomb protein complex 1 (PRC1) and methyl CpG binding protein 2 (MeCP2), at the COX-2 promoter in lung fibroblasts from patients with IPF (F-IPFs) can induce COX-2 expression silence. G9a and EZH2 and the Dnmt1 inhibitor markedly reduced H3K9me3 (49-79%), H3K27me3 (44-81%), and DNA methylation (61-97%) at the COX-2 promoter. These reductions were correlated with increased histone H3 and H4 acetylation, resulting in COX-2 mRNA and protein reexpression in F-IPFs." 24652950 A central role for G9a and EZH2 in the epigenetic silencing of cyclooxygenase-2 in idiopathic pulmonary fibrosis 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens PTGS2 5743 Gene mRNA dna methylation NA NA qRT-PCR; ELISA etc. no "Marked increases in H3K9me3, H3K27me3, and DNA methylation, together with their respective modifying enzymes G9a, EZH2, and DNA methyltransferases (Dnmts) and respective binding proteins heterochromatin protein 1 (HP1), polycomb protein complex 1 (PRC1) and methyl CpG binding protein 2 (MeCP2), at the COX-2 promoter in lung fibroblasts from patients with IPF (F-IPFs) can induce COX-2 expression silence. G9a and EZH2 and the Dnmt1 inhibitor markedly reduced H3K9me3 (49-79%), H3K27me3 (44-81%), and DNA methylation (61-97%) at the COX-2 promoter. These reductions were correlated with increased histone H3 and H4 acetylation, resulting in COX-2 mRNA and protein reexpression in F-IPFs." 24652950 A central role for G9a and EZH2 in the epigenetic silencing of cyclooxygenase-2 in idiopathic pulmonary fibrosis 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens SMURF2 64750 Gene mRNA up-regulation SMURF2 NA qRT-PCR; Dual-luciferase reporter assay; etc. no "Micrornas chips and real-time PCR confirmed in A549 EMT model has six, three cut micrornas, the expression level of miR - 424 through targeted Smurf2 enhance TGF - beta signaling pathways regulating muscle into fiber cell differentiation 6 up-regulated and 3 down-regulated miRNAs in a human lung epithelial cell EMT model were validated using miRNA microarray and real-time PCR. Up-regulated miR-424 regulates the myofibroblast differentiation during EMT by potentiating the TGF-B signaling pathway through Smurf2." 25524739 Regulation of myofibroblast differentiation by miR-424 during epithelial-to-mesenchymal transition 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens IGF1 3479 Gene mRNA down-regulation IGF-1 NA Dual-luciferase reporter assay; ELISA; qRT-PCR etc. no "MiR-130b-3p was downregulated in IPF lungs. MiR-130b-3p downregulation contributed to the activation of fibroblasts and the dysregulated epithelial-mesenchymal crosstalk by promoting IGF-1 secretion from lung epithelium, suggesting a key regulatory role for this miRNA in preventing lung fibrosis." 26953888 MiR-130b-3p Modulates Epithelial-Mesenchymal Crosstalk in Lung Fibrosis by Targeting IGF-1 2016 lung pulmonary_fibrosis homo_sapiens TGFBR1 7046 Gene mRNA dysregulation TGFBR1; TGFBR2 TGF-beta/SMAD signaling pathway qRT-PCR; Immunofluorescence etc. no "MiR-1343 reduces the expression of both TGF-B receptor 1 and 2 by directly targeting their 3'-UTRs. As a result, the abundance of fibrotic markers is reduced, cell migration into a scratch wound impaired and epithelial-to-mesenchymal transition (EMT) repressed. Mature miR-1343 is readily detected in human neutrophils and HL-60 cells and is activated in response to stress in A549 lung epithelial cells. MiR-1343 may have direct therapeutic applications in fibrotic lung disease." 26542979 MiR-1343 attenuates pathways of fibrosis by targeting the TGF-beta receptors 2016 lung pulmonary_fibrosis homo_sapiens TGFBR2 7048 Gene mRNA dysregulation TGFBR1; TGFBR2 TGF-beta/SMAD signaling pathway qRT-PCR; Immunofluorescence etc. no "MiR-1343 reduces the expression of both TGF-B receptor 1 and 2 by directly targeting their 3'-UTRs. As a result, the abundance of fibrotic markers is reduced, cell migration into a scratch wound impaired and epithelial-to-mesenchymal transition (EMT) repressed. Mature miR-1343 is readily detected in human neutrophils and HL-60 cells and is activated in response to stress in A549 lung epithelial cells. MiR-1343 may have direct therapeutic applications in fibrotic lung disease." 26542979 MiR-1343 attenuates pathways of fibrosis by targeting the TGF-beta receptors 2016 lung pulmonary_arterial_hypertension homo_sapiens PTPN11 5781 Gene mRNA down-regulation SHP2 STAT3-MIR-204-SRC-STAT3-NFAT signaling pathway TLDAS; qRT-PCR; Dual-luciferase reporter assay etc. no "MiR-204 expression in PASMCs is down-regulated in both human and rodent PAH. MiR-204 down-regulation correlates with PAH severity and accounts for the proliferative and antiapoptotic phenotypes of PAH-PASMCs. STAT3 activation suppresses miR-204 expression, and miR-204 directly targets SHP2 expression, thereby SHP2 up-regulation, by miR-204 down-regulation, activates the Src kinase and nuclear factor of activated T cells (NFAT). STAT3 also directly induces NFATc2 expression. NFAT and SHP2 were needed to sustain PAH-PASMC proliferation and resistance to apoptosis. Finally, delivery of synthetic miR-204 to the lungs of animals with PAH significantly reduced disease severity." 21321078 Role for miR-204 in human pulmonary arterial hypertension 2011 lung idiopathic_pulmonary_fibrosis homo_sapiens SMAD7 4092 Gene mRNA up-regulation SMAD7 NA Northern Blot; qRT-PCR; Dual-luciferase reporter assay etc. no "MiR-21 is up-regulated in the lungs of mice with bleomycin-induced fibrosis and also in the lungs of patients with IPF, and was primarily localized to myofibroblasts. Administration of miR-21 antisense probes diminished the severity of experimental lung fibrosis in mice, even when treatment was started 5-7 d after initiation of pulmonary injury. TGF-Beta1 enhanced miR-21 expression in primary pulmonary fibroblasts. Increasing miR-21 levels promoted, whereas knocking down miR-21 attenuated, the pro-fibrogenic activity of TGF-Beta1 in fibroblasts. A potential mechanism for the role of miR-21 in fibrosis is through regulating the expression of an inhibitory Smad, Smad7." 20643828 MiR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis 2010 lung cystic_fibrosis homo_sapiens CTSS 1520 Gene mRNA up-regulation IRF-1 MIR-31/IRF-1/CTSS signaling pathway ELISA; qRT-PCR etc. no "MiR-31, which is decreased in the CF airways, regulates IRF-1 in CF epithelial cells. Treating CF bronchial epithelial cells with a miR-31 mimic decreased IRF-1 protein levels with concomitant knockdown of CTSS expression and secretion." 24940638 MiR-31 dysregulation in cystic fibrosis airways contributes to increased pulmonary cathepsin S production 2014 lung cystic_fibrosis homo_sapiens IRF1 3659 Gene mRNA up-regulation IRF-1 MIR-31/IRF-1/CTSS signaling pathway ELISA; qRT-PCR etc. no "MiR-31, which is decreased in the CF airways, regulates IRF-1 in CF epithelial cells. Treating CF bronchial epithelial cells with a miR-31 mimic decreased IRF-1 protein levels with concomitant knockdown of CTSS expression and secretion." 24940638 MiR-31 dysregulation in cystic fibrosis airways contributes to increased pulmonary cathepsin S production 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens CCN4 8840 Gene mRNA up-regulation WISP1 NA qRT-PCR; Immunohistochemistry etc. no MiR-92a inhibt TGF-B1-induced WISP1 expression in pulmonary fibrosis. 24953558 MiR-92a regulates TGF-B1-induced WISP1 expression in pulmonary fibrosis 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP3 4314 Gene mRNA up-regulation NA NA Immunohistochemistry; Blood biomarker levels of MMP3; CXCL13 in a separate cohort of IPF patients etc. no MMP3 and CXCL13 are systemic biomarkers that reflect the aggregate burden of these pathological features across total lung tissue. These biomarkers may have clinical utility as prognostic and/or surrogate biomarkers of disease activity in interventional studies in IPF. 25217476 Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL13 10563 Gene mRNA up-regulation NA NA Immunohistochemistry; Blood biomarker levels of MMP3; CXCL13 in a separate cohort of IPF patients etc. no MMP3 and CXCL13 are systemic biomarkers that reflect the aggregate burden of these pathological features across total lung tissue. These biomarkers may have clinical utility as prognostic and/or surrogate biomarkers of disease activity in interventional studies in IPF. 25217476 Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP7 4316 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no MMP7 was previously shown to be a regulator and potentially predictive protein plasma biomarker in IPF. 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens FN1 2335 Gene mRNA up-regulation NA NA Immunohistochemistry; qRT-PCR etc. no "Next, we analyzed the expression of the well-characterized Wnt target genes fibronectin (Fn) 1, matrix metalloproteinase (Mmp) 7, and cyclin D1 in IPF lungs. As depicted in Figure 7b, all of these Wnt target genes were upregulated in IPF lung samples, as compared with transplant donor samples." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP7 4316 Gene mRNA up-regulation NA NA Immunohistochemistry; qRT-PCR etc. no "Next, we analyzed the expression of the well-characterized Wnt target genes fibronectin (Fn) 1, matrix metalloproteinase (Mmp) 7, and cyclin D1 in IPF lungs. As depicted in Figure 7b, all of these Wnt target genes were upregulated in IPF lung samples, as compared with transplant donor samples." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens CCND1 595 Gene mRNA up-regulation NA NA Immunohistochemistry; qRT-PCR etc. no "Next, we analyzed the expression of the well-characterized Wnt target genes fibronectin (Fn) 1, matrix metalloproteinase (Mmp) 7, and cyclin D1 in IPF lungs. As depicted in Figure 7b, all of these Wnt target genes were upregulated in IPF lung samples, as compared with transplant donor samples." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens CCNA2 890 Gene mRNA up-regulation NA NA qRT-PCR; ELISA; etc. no "One of the remarkable features of our study is the localization of increased CCNA2 expression to the alveolar epithelium, rather than to fibroblasts or myofibroblastic foci. CCNA2 is the main A-type cyclin present in somatic cells (36) and a mediator of the cell cycle. The overexpression and localization of CCNA2 to epithelial cells but not to mesenchymal cells suggests that IPF-AEx is probably an extension of the epithelial injury and dysregulation that characterizes IPF (37) and definitely is not a result of uncontrolled fibroblast proliferation." 19363140 Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis 2009 lung idiopathic_pulmonary_fibrosis homo_sapiens CCL13 6357 Gene mRNA up-regulation IGF-I NA qRT-PCR; Immunohistochemistry; Bleomycin exposure etc. no "Our gene expression profiling study identified several chemokines (CCL13, CXCL12, and CXCL14) and growth factors and their receptors (insulin-like growth factor-I [IGF-I], IGF-I-binding protein-5, and platelet-derived growth factor receptor-like) to be overexpressed in the lung specimens obtained from patients with IIP." 16998095 Gene expression profiling of familial and sporadic interstitial pneumonia 2007 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL14 9547 Gene mRNA up-regulation NA NA qRT-PCR; Immunohistochemistry; Bleomycin exposure etc. no "Our gene expression profiling study identified several chemokines (CCL13, CXCL12, and CXCL14) and growth factors and their receptors (insulin-like growth factor-I [IGF-I], IGF-I-binding protein-7, and platelet-derived growth factor receptor-like) to be overexpressed in the lung specimens obtained from patients with IIP." 16998095 Gene expression profiling of familial and sporadic interstitial pneumonia 2007 lung Pulmonary_Disease_Chronic_Obstructive homo_sapiens CXCL8 3576 Gene mRNA histone hyperacetylation NA NA qRT-PCR; HDAC activity assay etc. no Patients with COPD have a progressive reduction in total HDAC activity that reflects the severity of the disease; Specimens of lung tissue obtained from patients with increasing clinical stages of COPD had graded reductions in HDAC activity and increases in interleukin-8 messenger RNA (mRNA) and histone-4 acetylation at the interleukin-8 promoter. 15888697 Decreased histone deacetylase activity in chronic obstructive pulmonary disease 2005 lung idiopathic_pulmonary_fibrosis homo_sapiens POSTN 10631 Gene mRNA up-regulation NA NA BALF; Immunohistochemistry; ELISA etc. no "Periostin, a matrix protein, is a novel biomarker for idiopathic interstitial pneumonias." 21177844 "Periostin, a matrix protein, is a novel biomarker for idiopathic interstitial pneumonias" 2011 lung idiopathic_pulmonary_fibrosis homo_sapiens FOXJ1 2302 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "Recursive feature elimination using gene expression values identified FOXJ1, NELL2, SCGB3A1, LRRC34 and MYL3 as the top five most predictive genes (Fig 8D)." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens LRRC34 151827 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "Recursive feature elimination using gene expression values identified FOXJ1, NELL2, SCGB3A1, LRRC34 and MYL3 as the top five most predictive genes (Fig 8D)." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens MYL3 4634 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "Recursive feature elimination using gene expression values identified FOXJ1, NELL2, SCGB3A1, LRRC34 and MYL3 as the top five most predictive genes (Fig 8D)." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens NELL2 4753 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "Recursive feature elimination using gene expression values identified FOXJ1, NELL2, SCGB3A1, LRRC34 and MYL3 as the top five most predictive genes (Fig 8D)." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SCGB3A1 92304 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "Recursive feature elimination using gene expression values identified FOXJ1, NELL2, SCGB3A1, LRRC34 and MYL3 as the top five most predictive genes (Fig 8D)." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens LCN2 3934 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no "Remarkably, similar expression change intensities were found for several common differentially expressed genes in both species (Figure 2, Tables 2 and and3),3), such as matrix metallopeptidase 7 (MMP7/Mmp7; 9.2-fold in IPF, 21.1-fold in bleomycin), the phospholipase A2, group 2A (PLA2G2A/Pla2 g2a; 7.8-fold in IPF, 4.3-fold in bleomycin), lipocalin-2 (LCN2/Lcn2 4.6-fold in IPF, 3.5-fold in bleomycin), collagen triple helix repeat containing 1 (CTHRC1/Cthrc1; 4.3-fold in IPF, 3.2-fold in bleomycin), and complement component 6 (C6; 3.7-fold in IPF, 6.5-fold in bleomycin)." 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens C6 729 Gene mRNA up-regulation NA NA Cell Culture; Microarray Statistical Data Analysis; Gene Expression Analysis no "Remarkably, similar expression change intensities were found for several common differentially expressed genes in both species (Figure 2, Tables 2 and and3),3), such as matrix metallopeptidase 7 (MMP7/Mmp7; 9.2-fold in IPF, 21.1-fold in bleomycin), the phospholipase A2, group 2A (PLA2G2A/Pla2 g2a; 7.8-fold in IPF, 4.3-fold in bleomycin), lipocalin-2 (LCN2/Lcn2 4.6-fold in IPF, 3.5-fold in bleomycin), collagen triple helix repeat containing 1 (CTHRC1/Cthrc1; 4.3-fold in IPF, 3.2-fold in bleomycin), and complement component 6 (C6; 3.7-fold in IPF, 6.5-fold in bleomycin)." 25029475 A novel genomic signature with translational significance for human idiopathic pulmonary fibrosis 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens ROR2 4920 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway qRT-PCR; ELISA etc. no "ROR2 may be related to the development of IPF, and its protein level may be a useful and severity-dependent candidate marker for IPF." 32951408 Upregulation of receptor tyrosine kinase-like orphan receptor 2 in idiopathic pulmonary fibrosis 2020 lung idiopathic_pulmonary_fibrosis homo_sapiens S100A4 6275 Gene mRNA up-regulation NA NA qRT-PCR; ELISA; Immunofluorescence etc. no "S100A4 is expressed by alpha-SMA-positive cells in the interstitium of the IPF patients. S100A4 may participate in the development of IPF, and its protein level may be a candidate diagnostic and therapeutic marker for IPF." 32755764 The S100 calcium-binding protein A4 level is elevated in the lungs of patients with idiopathic pulmonary fibrosis 2020 lung idiopathic_pulmonary_fibrosis homo_sapiens IGFBP2 3485 Gene mRNA up-regulation NA IGF SIGNALLING PATHWAY Biomarkers measurements in serum; Pulmonary function tests; Statistical analysis etc. no Serum IGFBP-1 and -2 are increased in idiopathic pulmonary fibrosis and IGFBP-2 may be reduced by anti-fibrosing therapy. IGFBPs may be promising biomarkers in IPF. 27215343 Raised serum levels of IGFBP-1 and IGFBP-2 in idiopathic pulmonary fibrosis 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens IGFBP1 3484 Gene mRNA up-regulation NA IGF SIGNALLING PATHWAY Biomarkers measurements in serum; Pulmonary function tests; Statistical analysis etc. no Serum IGFBP-1 and -2 are increased in idiopathic pulmonary fibrosis and IGFBP-2 may be reduced by anti-fibrosing therapy. IGFBPs may be promising biomarkers in IPF. 27215343 Raised serum levels of IGFBP-1 and IGFBP-2 in idiopathic pulmonary fibrosis 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens SFTPD 6441 Gene mRNA up-regulation NA NA "Change in FVC and DLco, and definition of deterioration; Changes in SP-A, SP-D, and KL-6; Statistical analysis etc." no "Serum levels of SP-A, SP-D, and KL-6 have been shown to be useful in predicting prognosis and monitoring disease activity in patients with IPF." 32005219 Surfactant protein A as a biomarker of outcomes of anti-fibrotic drug therapy in patients with idiopathic pulmonary fibrosis 2020 lung idiopathic_pulmonary_fibrosis homo_sapiens MUC1 4582 Gene mRNA up-regulation NA NA "Change in FVC and DLco, and definition of deterioration; Changes in SP-A, SP-D, and KL-6; Statistical analysis etc." no "Serum levels of SP-A, SP-D, and KL-6 have been shown to be useful in predicting prognosis and monitoring disease activity in patients with IPF." 32005219 Surfactant protein A as a biomarker of outcomes of anti-fibrotic drug therapy in patients with idiopathic pulmonary fibrosis 2020 lung idiopathic_pulmonary_fibrosis homo_sapiens SFRP2 6423 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway qRT-PCR; Immunohistochemistry; Bleomycin exposure etc. no SFRP2 is almost fourfold upregulated in the diseased tissue. 16998095 Gene expression profiling of familial and sporadic interstitial pneumonia 2007 lung idiopathic_pulmonary_fibrosis homo_sapiens THY1 7070 Gene mRNA dna?hypermethylation NA NA qRT-PCR; Immunohistochemistry etc. no "Significant global hypermethylation was detected in hypoxic fibroblasts relative to normoxic controls and was accompanied by increased expression of myofibroblast markers. Thy-1 mRNA expression was suppressed in hypoxic cells, which was restored with the demethylating agent 5-aza-2'-deoxycytidine." 22938014 Hypoxia-induced DNA hypermethylation in human pulmonary fibroblasts is associated with Thy-1 promoter methylation and the development of a pro-fibrotic phenotype 2012 lung pulmonary_fibrosis homo_sapiens SMAD3 4088 Gene mRNA dna hypomethylation NA NA PCR; ELISA; Mass spectrometry etc. no "Smad3 gene hypomethylation might promote pulmonary fibrosis in Uygur PBL patients via increased Smad3 mRNA expression. Smad3 methylation, Smad3 mRNA expression and TGF-B level were correlated with the number of pigeons bred by patients." 28562330 The correlation between pulmonary fibrosis and methylation of peripheral Smad3 in cases of pigeon breeder's lung in a Chinese Uygur population 2017 lung idiopathic_pulmonary_fibrosis homo_sapiens SRF 6722 Gene mRNA up-regulation NA NA Data compilation; Statistical analysis etc. no "SRF is a transcription factor that is activated by the p38 MAP kinase pathway [24] and by increased extracellular matrix stiffness through mechanotransduction [25]. SRF is essential for collagen-1 expression by lung fibroblasts in vitro [26], while inhibition of the SRF pathway by the small molecule CCG-203971 attenuates lung fibrogenesis in the bleomycin-induced lung fibrosis model in mice [27]. Interestingly, SRF drives CTGF expression in fibroblasts [28], raising the hypothesis that the stable overexpression of the SRF/CTGF axis may contribute to the heritable profibrotic phenotype of lung fibroblasts in IPF." 27983601 Transcriptome of Cultured Lung Fibroblasts in Idiopathic Pulmonary Fibrosis: Meta-Analysis of Publically Available Microarray Datasets Reveals Repression of Inflammation and Immunity Pathways 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL12 6387 Gene mRNA up-regulation CXCR4 NA qRT-PCR; Immunohistochemistry; Bleomycin exposure etc. no "The chemokine CXCL12, or stromal cell-derived factor 1 (SDF-1), is an important regulator of hematopoietic cell development, migration, and proliferation, and is the only known ligand for the CXCR4 receptor." 16998095 Gene expression profiling of familial and sporadic interstitial pneumonia 2007 lung cystic_fibrosis homo_sapiens CFTR 1080 Gene mRNA up-regulation CFTR NA Dual-luciferase reporter assay; qRT-PCR; In situ Hybridization etc. no The Cystic Fibrosis Transmembrane conductance Regulator (CFTR) is a chloride channel that plays a critical role in the lung by maintaining fluid homeostasis. Absence or malfunction of CFTR leads to Cystic Fibrosis; Chronic cigarette smoking up-regulates miR-101 and that this miRNA could contribute to suppression of CFTR in the lungs of COPD patients. 23226399 MiR-101 and miR-144 regulate the expression of the CFTR chloride channel in the lung 2012 lung idiopathic_pulmonary_fibrosis homo_sapiens PTGER2 5732 Gene mRNA dna hypermethylation NA PTEN-AKT signaling pathway Global DNA methylation assay; qRT-PCR; Immunoblot etc. no The down-regulation of PTGER2 and consequent PGE2 resistance are both mediated by DNA hypermethylation; Increased Akt signal transduction as a novel mechanism that promotes DNA hypermethylation during fibrogenesis. 20889571 Hypermethylation of PTGER2 confers prostaglandin E2 resistance in fibrotic fibroblasts from humansand mice 2010 lung idiopathic_pulmonary_fibrosis homo_sapiens AGTR1 185 Gene mRNA up-regulation NA MKK1/MKK2 SIGNALLING PATHWAY qRT-PCR; Immunohistochemistry etc. no The finding that AGTR1 localizes to fibroblastic foci in IPF biopsies supports the potential relevance of the angiotensin system in this disease and suggests that the pro-fibrotic role of AGTR1 in IPF is not limited to epithelial cells [31]. Further studies are needed to assess the functional effects of AGTR1 stimulation in lung fibroblasts and to evaluate the biological role of AGTR1 in lung fibrosis. 15571627 Gene expression profiling reveals novel TGFbeta targets in adult lung fibroblasts 2004 lung idiopathic_pulmonary_fibrosis homo_sapiens IL33 90865 Gene mRNA up-regulation NA NA ELISA; Statistical analysis etc. no The IL-33 and TSLP levels in BAL fluids may be useful for differentiating IPF from other chronic interstitial lung diseases. 28202030 Upregulation of interleukin-33 and thymic stromal lymphopoietin levels in the lungs of idiopathic pulmonary fibrosis 2017 lung idiopathic_pulmonary_fibrosis homo_sapiens TSLP 85480 Gene mRNA up-regulation NA NA ELISA; Statistical analysis etc. no The IL-33 and TSLP levels in BAL fluids may be useful for differentiating IPF from other chronic interstitial lung diseases. 28202030 Upregulation of interleukin-33 and thymic stromal lymphopoietin levels in the lungs of idiopathic pulmonary fibrosis 2017 lung idiopathic_pulmonary_fibrosis homo_sapiens XCL1 6375 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CCL17 6361 Gene mRNA up-regulation CCR4 NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CCL5 6352 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL9 4283 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL10 3627 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL11 6373 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CCL15 6359 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL1 2919 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL6 6372 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CCL7 6354 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL17 284340 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL13 10563 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CCL14 6358 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL14 9547 Gene mRNA up-regulation NA NA "Identification of gene-expression subsets, principal component analysis and differential gene expression; Determination of ligand-receptor interactions using single cell RNA datasets; Development of pirfenidone response signature" no "The Myeloid-enriched IPF subset (Subset 1) had increased expression of XCL1, CCL17, CCL5, CXCL9, CXCL10 and CXCL11, whereas the Ciliated epithelium-enriched IPF subset (Subset 2) had increased expression of CCL15, CXCL1, CXCL6, CCL7, CXCL17, CXCL13, CCL14 and CXCL14." 33755690 Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TFPI 7035 Gene mRNA up-regulation NA NA ELISA; Immunohistochemistry etc. no The TF and TFPI levels in BAL fluid supernatant were significantly higher in IPF patients than in normal controls. 10946084 Relevance of tissue factor and tissue factor pathway inhibitor for hypercoagulable state in the lungs of patients with idiopathic pulmonary fibrosis 2000 lung cystic_fibrosis homo_sapiens TLR2 7097 Gene mRNA promoter hypomethylation NA NA Dual-luciferase reporter assay; qRT-PCR; etc. no TLR2 expression is epigenetically up-regulated via promoter hypomethylation in CF bronchial epithelial cells and suggest that TLR2 overexpression or prolonged activation of TLR2 signaling might be critical in CF pathogenesis. 16478769 Promoter hypomethylation of Toll-like receptor-2 gene is associated with increased proinflammatoryresponse toward bacterial peptidoglycan in cystic fibrosis bronchial epithelial cells 2006 lung idiopathic_pulmonary_fibrosis homo_sapiens NOX4 50507 Gene mRNA dysregulation TGFBR2; NOX4 NA Dual-luciferase reporter assay; ISH etc. no "Transforming growth factor-B1 (TGF-B1) stimulates the production of NADPH oxidase 4 (NOX4)-dependent ROS, promoting lung fibrosis (LF). MiR-9-5p has an inhibitory effect on TGF-B receptor type II (TGFBR2) and NOX4 expression. Increased expression of miR-9-5p abrogates TGF-B1-dependent myofibroblast phenotypic transformation. In the mouse model of bleomycin-induced LF, miR-9-5p dramatically reduces fibrogenesis and inhibition of miR-9-5p prevents its anti-fibrotic effect both in vitro and in vivo. In lung specimens from patients with IPF, high levels of miR-9-5p are found. TGF-B1 induces miR-9-5p expression as a self-limiting homeostatic response." 26315535 MiR-9-5p suppresses pro-fibrogenic transformation of fibroblasts and prevents organ fibrosis by targeting NOX4 and TGFBR2 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens TGFBR2 7048 Gene mRNA dysregulation TGFBR2; NOX4 NA Dual-luciferase reporter assay; ISH etc. no "Transforming growth factor-B1 (TGF-B1) stimulates the production of NADPH oxidase 4 (NOX4)-dependent ROS, promoting lung fibrosis (LF). MiR-9-5p has an inhibitory effect on TGF-B receptor type II (TGFBR2) and NOX4 expression. Increased expression of miR-9-5p abrogates TGF-B1-dependent myofibroblast phenotypic transformation. In the mouse model of bleomycin-induced LF, miR-9-5p dramatically reduces fibrogenesis and inhibition of miR-9-5p prevents its anti-fibrotic effect both in vitro and in vivo. In lung specimens from patients with IPF, high levels of miR-9-5p are found. TGF-B1 induces miR-9-5p expression as a self-limiting homeostatic response." 26315535 MiR-9-5p suppresses pro-fibrogenic transformation of fibroblasts and prevents organ fibrosis by targeting NOX4 and TGFBR2 2015 lung idiopathic_pulmonary_fibrosis homo_sapiens LIN28B 389421 Gene mRNA dysregulation LIN28B NA Masson's trichrome staining; Immunohistochemistry; qRT-PCR etc. no Upregulation of Lin28B contributes to idiopathic pulmonary fibrosis. Lin28B causes epithelial-mesenchymal transition (EMT) by inhibition of let-7d. Lin28B is one of the targets of microRNA-26a. MiR-26a enhances the expression of let-7d via targeting regulation of Lin28B. A regulatory network among miRNAs involved in the progression of IPF. 26787543 MiR-26a suppresses EMT by disrupting the Lin28B/let-7d axis: potential cross-talks among miRNAs in IPF 2016 lung idiopathic_pulmonary_fibrosis homo_sapiens FOXO3 2309 Gene mRNA up-regulation FOXO3A NA qRT-PCR; In Situ Hybridization For miR-96 etc. no "When IPF fibroblasts interact with collagen-rich matrix, pathologically increased miR-96 expression inhibits FoxO3a function, causing IPF fibroblasts to maintain their pathological phenotype, which may contribute to the progression of IPF." 25172912 MicroRNA-96 inhibits FoxO3a function in IPF fibroblasts on type I collagen matrix 2014 lung idiopathic_pulmonary_fibrosis homo_sapiens CCN4 8840 Gene mRNA up-regulation NA NA qRT-PCR; Immunohistochemistry; etc. no "WISP1 enhanced fibrogenesis by inducing EMT of ATII cells and increasing collagen production by fibroblasts, indicating that WISP1 exerts its profibrotic effects by a multitude of autocrine and paracrine effects in the lung." 19287097 WNT1-inducible signaling protein-1 mediates pulmonary fibrosis in mice and is upregulated in humans with idiopathic pulmonary fibrosis 2009 lung idiopathic_pulmonary_fibrosis homo_sapiens FZD2 2535 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no "Wnt1, 7b and 10b, Fzd2 and 3, beta-catenin, and Lef4 expression was significantly increased in IPF." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens FZD3 7976 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no "Wnt1, 7b and 10b, Fzd2 and 3, beta-catenin, and Lef4 expression was significantly increased in IPF." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens CTNNB1 1499 Gene mRNA up-regulation NA WNT/B-CATENIN signaling pathway Immunohistochemistry; qRT-PCR etc. no "Wnt1, 7b and 10b, Fzd2 and 3, beta-catenin, and Lef4 expression was significantly increased in IPF." 18478089 Functional Wnt signaling is increased in idiopathic pulmonary fibrosis 2008 lung idiopathic_pulmonary_fibrosis homo_sapiens ARHGEF3 50650 Gene mRNA histone acetylation NA NA qRT-PCR; Immunohistochemistry etc. no "XPLN depletion stimulated SPARC expression and Akt phosphorylation on Ser473. TGF-B1 treatment down-regulated XPLN via Smad 2/3. XPLN mRNA expression was up-regulated upon treatment with HDAC inhibitors in a concentration-dependent manner, and TGF-B1-induced SPARC expression was reversed by entinostat treatment. MTORC1 inhibition by rapamycin and Raptor depletion stimulated SPARC expression." 28315487 XPLN is modulated by HDAC inhibitors and negatively regulates SPARC expression by targeting mTORC2 in human lung fibroblasts 2017 lung idiopathic_pulmonary_fibrosis homo_sapiens SPARC 6678 Gene mRNA histone acetylation NA NA qRT-PCR; Immunohistochemistry etc. no "XPLN depletion stimulated SPARC expression and Akt phosphorylation on Ser473. TGF-B1 treatment down-regulated XPLN via Smad 2/3. XPLN mRNA expression was up-regulated upon treatment with HDAC inhibitors in a concentration-dependent manner, and TGF-B1-induced SPARC expression was reversed by entinostat treatment. MTORC1 inhibition by rapamycin and Raptor depletion stimulated SPARC expression." 28315487 XPLN is modulated by HDAC inhibitors and negatively regulates SPARC expression by targeting mTORC2 in human lung fibroblasts 2017 pancreas pancreatitis homo_sapiens NFKB1 4790 Gene mRNA up-regulation SURVIVIN; CIAP1 NA qRT-PCR; rela transcription factor assay no "Islets in cp not only evade immune attack by nonexposure of functional death receptors in the presence of trail-r4 but also additionally neoexpress nfkappab and its target genes, survivin and ciap1, to protect themselves from apoptosis." 16127431 Parenchymal regression in chronic pancreatitis spares islets reprogrammed for the expression of NFkappaB and IAPs 2005 pancreas pancreatitis homo_sapiens BIRC3 330 Gene mRNA up-regulation SURVIVIN; CIAP1 NA qRT-PCR; rela transcription factor assay no "Islets in cp not only evade immune attack by nonexposure of functional death receptors in the presence of trail-r4 but also additionally neoexpress nfkappab and its target genes, survivin and ciap1, to protect themselves from apoptosis." 16127431 Parenchymal regression in chronic pancreatitis spares islets reprogrammed for the expression of NFkappaB and IAPs 2005 pancreas pancreatitis homo_sapiens NOTCH-2 4853 Gene mRNA dysregulation NA NOTCH SIGNALING PATHWAY qRT-PCR; immunohistochemistry no "These findings suggest a possible role of the notch pathway during pancreatic regeneration since jagged-1 inhibits inducible collagen-1 production, suggesting a new mechanism of tissue repair in this disease." 17114010 Pancreatic regeneration in chronic pancreatitis requires activation of the notch signaling pathway 2006 pancreas pancreatitis homo_sapiens NOTCH-3 4854 Gene mRNA dysregulation NA NOTCH SIGNALING PATHWAY qRT-PCR; immunohistochemistry no "These findings suggest a possible role of the notch pathway during pancreatic regeneration since jagged-1 inhibits inducible collagen-1 production, suggesting a new mechanism of tissue repair in this disease." 17114010 Pancreatic regeneration in chronic pancreatitis requires activation of the notch signaling pathway 2006 pancreas pancreatitis homo_sapiens NOTCH-4 4855 Gene mRNA dysregulation NA NOTCH SIGNALING PATHWAY qRT-PCR; immunohistochemistry no "These findings suggest a possible role of the notch pathway during pancreatic regeneration since jagged-1 inhibits inducible collagen-1 production, suggesting a new mechanism of tissue repair in this disease." 17114010 Pancreatic regeneration in chronic pancreatitis requires activation of the notch signaling pathway 2006 pancreas cystic_fibrosis homo_sapiens CFTR 1080 Gene mRNA dysregulation NA NA NA no "We conclude that severe reduction in cftr mrna causes cf, but can have different consequences in the lung and pancreas." 1721624 Severe deficiency of cystic fibrosis transmembrane conductance regulator messenger RNA carrying nonsense mutations R553X and W1316X in respiratory epithelial cells of patients with cystic fibrosis 1991 pancreas cystic_fibrosis homo_sapiens W1316X NA NA mRNA dysregulation NA NA NA no "We conclude that severe reduction in cftr mrna causes cf, but can have different consequences in the lung and pancreas." 1721624 Severe deficiency of cystic fibrosis transmembrane conductance regulator messenger RNA carrying nonsense mutations R553X and W1316X in respiratory epithelial cells of patients with cystic fibrosis 1991 skin scleroderma_systemic homo_sapiens CCR7 1236 Gene mRNA dysregulation NA NA RT-PCR no "We could confirm data of previous studies indicating that gene expression of il-6 is up-regulated in ls lesions as compared to healthy skin. Moreover, we have shown for the first time a significant increase of mrna levels of ccr7 and ccl5;Rantes in ls lesions indicating an important pathogenetic role of chemokines in ls." 21616095 Significantly increased CCL5/RANTES and CCR7 mRNA levels in localized scleroderma 2011 lung idiopathic_pulmonary_fibrosis homo_sapiens LGALS3 3958 Gene mRNA up-regulation NA NA Fluorescence intensity yes "Galectin (Gal)-3 is a central regulator of fibrosis in the lung with expression upregulated in bronchoalveolar lavage (BAL) fluid and serum of IPF patients, and further elevation observed during exacerbations. The profibrotic function of Gal-3 is multifactorial due to its ability to cross-link and promote signalling via multiple cell surface receptors including integrins and growth factor receptors, such as transforming growth factor-beta, vascular endothelial growth factor and platelet-derived growth factor (PDGF) receptors. Constitutive global deficiency of Gal-3 leads to attenuated fibrosis in murine models." 33214209 Target inhibition of galectin-3 by inhaled TD139 in patients with idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens NES 10763 Gene mRNA up-regulation TbetaRI TGF-BETA SIGNALING PATHWAY qRT-PCR; Immunohistochemistry; Immunofluorescence etc. no "Nestin regulates the vesicular trafficking system by promoting recycling of TbetaRI to the cell membrane through Rab11 and thereby contributes to the progression of pulmonary fibrosis. More importantly, precise targeting of Nestin expression within lung myofibroblasts can alleviate lung fibrogenesis and may represent a potential therapeutic strategy for IPF." 34625478 Nestin promotes pulmonary fibrosis?via?facilitating recycling of TGF-beta receptor I 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens IGF1 3479 Gene mRNA up-regulation NA IGF1 SIGNALING PATHWAY ELISA; Immunofluorescence; RT-PCR etc. no "Western blotting showed that the levels of IGF1, IGFR-1, PI3K, AKT and p-AKT in lung tissues of patients with IPF were significantly higher than those in normal lung tissues. This indicated that the IGF1 signaling pathway is activated in IPF conditions." 34329195 Regulation of the IGF1 signaling pathway is involved in idiopathic pulmonary fibrosis induced by alveolar epithelial cell senescence and core fucosylation 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CDKN1A 1026 Gene mRNA up-regulation NA NA ELISA; Immunofluorescence; RT-PCR etc. no Immunofluorescence showed that there were significantly increased expression of senescence key protein (P21) in AECs and the increased p21 were accompanied by up-regulated CF (as indicated by FUT8 and LCA levels). 34329195 Regulation of the IGF1 signaling pathway is involved in idiopathic pulmonary fibrosis induced by alveolar epithelial cell senescence and core fucosylation 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CDKN2A 1029 Gene mRNA up-regulation NA NA ELISA; immunofluorescence; RT-PCR etc. no "Western blotting also showed that the levels of senescence key protein (P21, P16) and FUT8 were upregulated in IPF lung tissue." 34329195 Regulation of the IGF1 signaling pathway is involved in idiopathic pulmonary fibrosis induced by alveolar epithelial cell senescence and core fucosylation 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens FUT8 2530 Gene mRNA up-regulation NA NA ELISA; immunofluorescence; RT-PCR etc. no "Western blotting also showed that the levels of senescence key protein (P21, P16) and FUT8 were upregulated in IPF lung tissue." 34329195 Regulation of the IGF1 signaling pathway is involved in idiopathic pulmonary fibrosis induced by alveolar epithelial cell senescence and core fucosylation 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CFL1 1072 Gene mRNA up-regulation NA NA qRT-PCR; Western Blot etc. no "Compared with that of healthy controls, the expression of CFL-1 was significantly increased in the plasma and peripheral blood mononuclear cells (PBMCs) from idiopathic pulmonary fibrosis (IPF) and connective tissue disease-associated interstitial lung disease (CTD-ILD) patients (P < 0.05)." 34090209 Cofilin-1 promotes fibrocyte differentiation and contributes to pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SIRT2 22933 Gene mRNA up-regulation Smad2; Smad3 Smad2/3 pathway RT-PCR; Western Blot; Immunofluorescence etc. no Sirt2 expression was upregulated in transforming growth factor-beta1 (TGF-beta1) treated human embryonic lung fibroblasts. 34925016 Inhibition of Sirt2 Alleviates Fibroblasts Activation and Pulmonary Fibrosis?via?Smad2/3 Pathway 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens MDM4 4194 Gene mRNA up-regulation TP53 Mdm4-p53 pathway qRT-PCR; ELISA; Flow Cytometry etc. no "In this study, we found that mouse double minute 4 homolog (MDM4) is highly expressed in the fibrotic lesions of human IPF and experimental pulmonary fibrosis in aged mice." 33688918 Targeting mechanosensitive MDM4 promotes lung fibrosis resolution in aged mice 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SIRT3 23410 Gene mRNA down-regulation NA NA PCR; Western Blot etc. no "We showed that sirtuin 3 (SIRT3), a mitochondrial protein regulating cell fate and aging, is deficient in the AECs of idiopathic pulmonary fibrosis (IPF) patients and that asbestos- and bleomycin-induced lung fibrosis is augmented in Sirt3 knockout (Sirt3-/-) mice associated with AEC mtDNA damage and intrinsic apoptosis." 34202229 "SIRT3 Overexpression Ameliorates Asbestos-Induced Pulmonary Fibrosis, mt-DNA Damage, and Lung Fibrogenic Monocyte Recruitment" 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens IL22 50616 Gene mRNA down-regulation NA TGF-BETA SIGNALING PATHWAY qRT-PCR; Enzyme-linked Immunosorbent Assay; Western Blot etc. no The expression of IL-22 was lower in the peripheral blood of IPF patients and correlated negatively with the disease severity. 34459137 Protective function of interleukin-22 in pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens MYRF 745 Gene mRNA down-regulation NA NA co-expression gene pair analysis; functional enrichment analysis etc. no "A total of 343 DEGs and 21 DEMs were identified between IPF and normal samples. CLDN18, COL6A3, MYRF, PRSS8, RRAS, and SBNO1 were identified as potential IPF biomarkers. In addition, 17 miRNA-target relationship pairs were obtained. The up-regulation of hsa-miR-657, hsa-miR-671-5p, hsa-miR-198, and hsa-miR-940 could regulate the down-regulation of MYRF and the up-regulation of hsa-miR-198 and hsa-miR-373-3p could regulate the down-regulation of RRAS and CLDN18, respectively. Our data indicated that PRSS8, hsa-miR-614, and hsa-miR-503-5p might be involved in the migration and invasion of IPF related cells." 34666057 Screening of Biomarkers Involved in Idiopathic Pulmonary Fibrosis and Regulation of Upstream miRNAs 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens CLDN18 51208 Gene mRNA down-regulation NA NA co-expression gene pair analysis; functional enrichment analysis etc. no "A total of 343 DEGs and 21 DEMs were identified between IPF and normal samples. CLDN18, COL6A3, MYRF, PRSS8, RRAS, and SBNO1 were identified as potential IPF biomarkers. In addition, 17 miRNA-target relationship pairs were obtained. The up-regulation of hsa-miR-657, hsa-miR-671-5p, hsa-miR-198, and hsa-miR-940 could regulate the down-regulation of MYRF and the up-regulation of hsa-miR-198 and hsa-miR-373-3p could regulate the down-regulation of RRAS and CLDN18, respectively. Our data indicated that PRSS8, hsa-miR-614, and hsa-miR-503-5p might be involved in the migration and invasion of IPF related cells." 34666057 Screening of Biomarkers Involved in Idiopathic Pulmonary Fibrosis and Regulation of Upstream miRNAs 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens COL6A3 1293 Gene mRNA dysregulation NA NA co-expression gene pair analysis; functional enrichment analysis etc. no "A total of 343 DEGs and 21 DEMs were identified between IPF and normal samples. CLDN18, COL6A3, MYRF, PRSS8, RRAS, and SBNO1 were identified as potential IPF biomarkers. In addition, 17 miRNA-target relationship pairs were obtained. The up-regulation of hsa-miR-657, hsa-miR-671-5p, hsa-miR-198, and hsa-miR-940 could regulate the down-regulation of MYRF and the up-regulation of hsa-miR-198 and hsa-miR-373-3p could regulate the down-regulation of RRAS and CLDN18, respectively. Our data indicated that PRSS8, hsa-miR-614, and hsa-miR-503-5p might be involved in the migration and invasion of IPF related cells." 34666057 Screening of Biomarkers Involved in Idiopathic Pulmonary Fibrosis and Regulation of Upstream miRNAs 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens PRSS8 5652 Gene mRNA dysregulation NA NA co-expression gene pair analysis; functional enrichment analysis etc. no "A total of 343 DEGs and 21 DEMs were identified between IPF and normal samples. CLDN18, COL6A3, MYRF, PRSS8, RRAS, and SBNO1 were identified as potential IPF biomarkers. In addition, 17 miRNA-target relationship pairs were obtained. The up-regulation of hsa-miR-657, hsa-miR-671-5p, hsa-miR-198, and hsa-miR-940 could regulate the down-regulation of MYRF and the up-regulation of hsa-miR-198 and hsa-miR-373-3p could regulate the down-regulation of RRAS and CLDN18, respectively. Our data indicated that PRSS8, hsa-miR-614, and hsa-miR-503-5p might be involved in the migration and invasion of IPF related cells." 34666057 Screening of Biomarkers Involved in Idiopathic Pulmonary Fibrosis and Regulation of Upstream miRNAs 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens RRAS 6237 Gene mRNA dysregulation NA NA co-expression gene pair analysis; functional enrichment analysis etc. no "A total of 343 DEGs and 21 DEMs were identified between IPF and normal samples. CLDN18, COL6A3, MYRF, PRSS8, RRAS, and SBNO1 were identified as potential IPF biomarkers. In addition, 17 miRNA-target relationship pairs were obtained. The up-regulation of hsa-miR-657, hsa-miR-671-5p, hsa-miR-198, and hsa-miR-940 could regulate the down-regulation of MYRF and the up-regulation of hsa-miR-198 and hsa-miR-373-3p could regulate the down-regulation of RRAS and CLDN18, respectively. Our data indicated that PRSS8, hsa-miR-614, and hsa-miR-503-5p might be involved in the migration and invasion of IPF related cells." 34666057 Screening of Biomarkers Involved in Idiopathic Pulmonary Fibrosis and Regulation of Upstream miRNAs 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens SBNO1 55206 Gene mRNA dysregulation NA NA co-expression gene pair analysis; functional enrichment analysis etc. no "A total of 343 DEGs and 21 DEMs were identified between IPF and normal samples. CLDN18, COL6A3, MYRF, PRSS8, RRAS, and SBNO1 were identified as potential IPF biomarkers. In addition, 17 miRNA-target relationship pairs were obtained. The up-regulation of hsa-miR-657, hsa-miR-671-5p, hsa-miR-198, and hsa-miR-940 could regulate the down-regulation of MYRF and the up-regulation of hsa-miR-198 and hsa-miR-373-3p could regulate the down-regulation of RRAS and CLDN18, respectively. Our data indicated that PRSS8, hsa-miR-614, and hsa-miR-503-5p might be involved in the migration and invasion of IPF related cells." 34666057 Screening of Biomarkers Involved in Idiopathic Pulmonary Fibrosis and Regulation of Upstream miRNAs 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP1 4312 Gene mRNA up-regulation NA MAPK PATHWAY GO and pathway enrichment analysis etc. no "MMP1, SPP1, and BPIFB1 were the top three DEGs with the highest significant up-regulation. These DEGs played an important role in the occurrence of IPF through the MAPK (mitogen-activated protein kinase) signaling pathway." 34734011 Bioinformatic analysis of differentially expressed genes and pathways in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SPP1 6696 Gene mRNA up-regulation NA MAPK PATHWAY GO and pathway enrichment analysis etc. no "MMP1, SPP1, and BPIFB1 were the top three DEGs with the highest significant up-regulation. These DEGs played an important role in the occurrence of IPF through the MAPK (mitogen-activated protein kinase) signaling pathway." 34734011 Bioinformatic analysis of differentially expressed genes and pathways in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens BPIFB1 92747 Gene mRNA up-regulation NA MAPK PATHWAY GO and pathway enrichment analysis etc. no "MMP1, SPP1, and BPIFB1 were the top three DEGs with the highest significant up-regulation. These DEGs played an important role in the occurrence of IPF through the MAPK (mitogen-activated protein kinase) signaling pathway." 34734011 Bioinformatic analysis of differentially expressed genes and pathways in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens GABARAPL1 23710 Gene mRNA down-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no "By combining the PPI network, miRNA-target network, and functional enrichment analysis, we identified potential biomarkers including GABARAPL1, SGTA, ARRB1, GPX8, and VCAM1 for IPF. Among them, GABARAPL1, SGTA, and ARRB1 exhibited lower expression levels in IPF while GPX8 and VCAM1 were both downregulated in IPF." 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens GPX8 493869 Gene mRNA up-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no "In the network, there were 227 nodes, including 122 upregulated and 105 downregulated genes. Nodes with degree >= 7 were considered hub genes, including GABARAPL1, GPX8, SGTA, VCAM1, ARRB1, SPP1, and HLA-B." 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SGTA 6449 Gene mRNA down-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no "By combining the PPI network, miRNA-target network, and functional enrichment analysis, we identified potential biomarkers including GABARAPL1, SGTA, ARRB1, GPX8, and VCAM1 for IPF. Among them, GABARAPL1, SGTA, and ARRB1 exhibited lower expression levels in IPF while GPX8 and VCAM1 were both downregulated in IPF." 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens VCAM1 7412 Gene mRNA up-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no "In the network, there were 227 nodes, including 122 upregulated and 105 downregulated genes. Nodes with degree >= 7 were considered hub genes, including GABARAPL1, GPX8, SGTA, VCAM1, ARRB1, SPP1, and HLA-B." 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens ARRB1 408 Gene mRNA down-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no "By combining the PPI network, miRNA-target network, and functional enrichment analysis, we identified potential biomarkers including GABARAPL1, SGTA, ARRB1, GPX8, and VCAM1 for IPF. Among them, GABARAPL1, SGTA, and ARRB1 exhibited lower expression levels in IPF while GPX8 and VCAM1 were both downregulated in IPF." 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SPP1 6696 Gene mRNA up-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no "In the network, there were 227 nodes, including 122 upregulated and 105 downregulated genes. Nodes with degree >= 7 were considered hub genes, including GABARAPL1, GPX8, SGTA, VCAM1, ARRB1, SPP1, and HLA-B." 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens HLA-B 3106 Gene mRNA down-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no "In the network, there were 227 nodes, including 122 upregulated and 105 downregulated genes. Nodes with degree >= 7 were considered hub genes, including GABARAPL1, GPX8, SGTA, VCAM1, ARRB1, SPP1, and HLA-B." 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens LDLR 3949 Gene mRNA up-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no We found that LDLR and RAB11FIP1 were regulated by most miRNAs. Both were upregulated in IPF_S compared to N_CTL. 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens RAB11FIP1 80223 Gene mRNA up-regulation NA NA Differentially Expressed Analysis; Western Blot etc. no We found that LDLR and RAB11FIP1 were regulated by most miRNAs. Both were upregulated in IPF_S compared to N_CTL. 34285914 Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP7 4316 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Some genes that were up-regulated in fibrosis samples, such as MMP7, TNF, and PLAU, were genes involved in the tissue repair process." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TNF 7124 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Some genes that were up-regulated in fibrosis samples, such as MMP7, TNF, and PLAU, were genes involved in the tissue repair process." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens PLAU 5328 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Some genes that were up-regulated in fibrosis samples, such as MMP7, TNF, and PLAU, were genes involved in the tissue repair process." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TGFBI 7045 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "TGFBI, a gene that is known to participate in the EMT process, is up-regulated in fibrosis." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP11 4320 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Genes involved in coagulation, such as MMP7 and MMP11, as well as genes involved in EMT, such as COL3A1, COL1A1, and ADAM12 were also up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens COL3A1 1281 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Genes involved in coagulation, such as MMP7 and MMP11, as well as genes involved in EMT, such as COL3A1, COL1A1, and ADAM12 were also up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens COL1A1 1277 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Genes involved in coagulation, such as MMP7 and MMP11, as well as genes involved in EMT, such as COL3A1, COL1A1, and ADAM12 were also up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens ADAM12 8038 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Genes involved in coagulation, such as MMP7 and MMP11, as well as genes involved in EMT, such as COL3A1, COL1A1, and ADAM12 were also up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CD28 940 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "CD28 and CD86 were up-regulated, and CD274 (encoding the co-inhibitory receptor PD-L1) were down-regulated in both minimal and established fibrosis." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CD86 942 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "CD28 and CD86 were up-regulated, and CD274 (encoding the co-inhibitory receptor PD-L1) were down-regulated in both minimal and established fibrosis." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CD274 29126 Gene mRNA down-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "CD28 and CD86 were up-regulated, and CD274 (encoding the co-inhibitory receptor PD-L1) were down-regulated in both minimal and established fibrosis." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TLR4 7099 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "In our IPF samples, TLRs that could recognize both bacteria (TLR4 and TLR6) and viruses (TLR7 and TLR8) were significantly up-regulated. Of the remainder of the TLRs, only TLR2 was down-regulated, and almost all other TLRs were up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TLR6 10333 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "In our IPF samples, TLRs that could recognize both bacteria (TLR4 and TLR6) and viruses (TLR7 and TLR8) were significantly up-regulated. Of the remainder of the TLRs, only TLR2 was down-regulated, and almost all other TLRs were up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TLR7 51284 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "In our IPF samples, TLRs that could recognize both bacteria (TLR4 and TLR6) and viruses (TLR7 and TLR8) were significantly up-regulated. Of the remainder of the TLRs, only TLR2 was down-regulated, and almost all other TLRs were up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TLR8 51311 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "In our IPF samples, TLRs that could recognize both bacteria (TLR4 and TLR6) and viruses (TLR7 and TLR8) were significantly up-regulated. Of the remainder of the TLRs, only TLR2 was down-regulated, and almost all other TLRs were up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TLR2 7097 Gene mRNA down-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "In our IPF samples, TLRs that could recognize both bacteria (TLR4 and TLR6) and viruses (TLR7 and TLR8) were significantly up-regulated. Of the remainder of the TLRs, only TLR2 was down-regulated, and almost all other TLRs were up-regulated." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens NFKB1 4790 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Their downstream targets, including components of the NFKB pathway, such as NFKB1, TRAF3, PKD1, and CYLD, were also up-regulated in the IPF samples." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TRAF3 7187 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Their downstream targets, including components of the NFKB pathway, such as NFKB1, TRAF3, PKD1, and CYLD, were also up-regulated in the IPF samples." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens PKD1 5310 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Their downstream targets, including components of the NFKB pathway, such as NFKB1, TRAF3, PKD1, and CYLD, were also up-regulated in the IPF samples." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CYLD 1540 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Their downstream targets, including components of the NFKB pathway, such as NFKB1, TRAF3, PKD1, and CYLD, were also up-regulated in the IPF samples." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TGFB1 7040 Gene mRNA up-regulation TGFBR1 NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Important transforming growth factors, namely TGFB1, TGFB2, and TGFB3 and their receptor TGFBR1, were all up-regulated starting from the minimal fibrosis ." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TGFB2 7042 Gene mRNA up-regulation TGFBR1 NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Important transforming growth factors, namely TGFB1, TGFB2, and TGFB3 and their receptor TGFBR1, were all up-regulated starting from the minimal fibrosis ." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TGFB3 7043 Gene mRNA up-regulation TGFBR1 NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Important transforming growth factors, namely TGFB1, TGFB2, and TGFB3 and their receptor TGFBR1, were all up-regulated starting from the minimal fibrosis ." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens TGFBR1 7046 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Important transforming growth factors, namely TGFB1, TGFB2, and TGFB3 and their receptor TGFBR1, were all up-regulated starting from the minimal fibrosis ." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CASP1 834 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Additionally, CASP1, NLRC4, which participate in the activation of a cytokine storm, were all up-regulated in minimal fibrosis, while another cytokine storm trigger, IL18, was up-regulated in both minimal and established fibrosis regions." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens NLRC4 58484 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Additionally, CASP1, NLRC4, which participate in the activation of a cytokine storm, were all up-regulated in minimal fibrosis, while another cytokine storm trigger, IL18, was up-regulated in both minimal and established fibrosis regions." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens IL18 3606 Gene mRNA up-regulation NA NA Histological Analyses; Pre-operative MDCT Analyses etc. no "Additionally, CASP1, NLRC4, which participate in the activation of a cytokine storm, were all up-regulated in minimal fibrosis, while another cytokine storm trigger, IL18, was up-regulated in both minimal and established fibrosis regions." 33862585 The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF) 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens IGF1 3479 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SPP1 6696 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens PROM1 8842 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SOX2 6657 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP1 4312 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens COL1A1 1277 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens MMP7 4316 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens POSTN 10631 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens COL3A1 1281 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens COMP 1311 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens LCN2 3934 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens IL6 3569 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens VEGFA 7422 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CDH5 1003 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens WNT3A 89780 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens ICAM1 3383 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens EDN1 1906 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CSF3 1440 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CAV1 857 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens HBEGF 1839 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "The 20 hub genes comprised 11 upregulated (IGF1, SPP1, PROM1, SOX2, MMP1, COL1A1, MMP7, POSTN, COL3A1, COMP, LCN2) and nine downregulated (IL6, VEGFA, CDH5, WNT3A, ICAM1, EDN1, CSF3, CAV1, HBEGF) genes." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CXCL14 9547 Gene mRNA up-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens DAPK2 23604 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens EMP2 2013 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens GPM6A 2823 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens STXBP6 29091 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens LRRC32 2615 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens ADRB1 153 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SLC6A4 6532 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens CCDC85A 114800 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens FOXF1 2294 Gene mRNA down-regulation NA NA GO and KEGG enrichment analysis; GSVA; Hub gene analysis etc. no "We identified 13 miRNAs (miR-107, miR-125a-5p, miR-133b, miR-140-5p, miR-142-3p, miR-199a-3p, miR-199a-5p, miR-199b-5p, miR-28-5p, miR-324-5p, miR-34c-5p, miR-429, and miR-520b) and 13 mRNAs (WNT3A, CDH5, DAPK2, EMP2, GPM6A, STXBP6, VEGFA, LRRC32, ADRB1, SLC6A4, CCDC85A, FOXF1, and CXCL14). All miRNAs were upregulated except miR-520b. All genes for these mRNAs were downregulated except CXCL14." 34522168 Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens ASS1 445 Gene mRNA down-regulation NA NA qRT-PCR; Immunofluorescence; Flow Cytometry Assay etc. no "Compared to normal lung tissues, low ASS1 was detected in 73% (n =22/30) of ILD specimens (p < 0.0001). Likewise, a decline of ASS1 signal was found in the tissue sections from IPF patients, whereas more intense ASS1 staining was observed in normal lung tissues." 33508432 Therapeutic targeting of argininosuccinate synthase 1 (ASS1)-deficient pulmonary fibrosis 2021 lung respiratory_distress_syndrome_acute homo_sapiens BCL2 596 Gene mRNA up-regulation NA NA Western Blot; qRT-PCR etc. no "Western blotting and RT-qRT-PCR results showed that Bcl-2 expressions increased significantly after LPS stimulation in the LPS group as compared with the blank control group, and caspase-3 expressions decreased significantly." 34412758 Overexpression of mitofusion 2 inhibits acute respiratory distress syndrome pulmonary fibrosis and its mechanism 2021 lung respiratory_distress_syndrome_acute homo_sapiens CASP3 836 Gene mRNA down-regulation NA NA Western Blot; qRT-PCR etc. no "Western blotting and RT-qRT-PCR results showed that Bcl-2 expressions increased significantly after LPS stimulation in the LPS group as compared with the blank control group, and caspase-3 expressions decreased significantly." 34412758 Overexpression of mitofusion 2 inhibits acute respiratory distress syndrome pulmonary fibrosis and its mechanism 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens GREM2 64388 Gene mRNA up-regulation NA NA Immunohistochemistry; Immunofluorescence; qRT-PCR etc. no Gremlin2 was highly expressed in the serum and lung tissues in IPF patients. Bleomycin-induced lung fibrosis model exhibited high expression of Gremlin2 in the bronchoalveolar lavage fluid (BALF) and lung tissue. 34422900 Gremlin2 Activates Fibroblasts to Promote Pulmonary Fibrosis Through the Bone Morphogenic Protein Pathway 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SPP1 6696 Gene mRNA up-regulation NA NA Histological Analysis; qRT-PCR etc. no "Osteopontin (OPN), a matricellular protein with proinflammatory and profibrotic properties, plays a major role in several fibrotic diseases, including IPF; OPN is highly upregulated in patients' lung samples." 34243624 Osteopontin silencing attenuates bleomycin-induced murine pulmonary fibrosis by regulating epithelial-mesenchymal transition 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens SOX9 6662 Gene mRNA up-regulation NA NA Immunohistochemistry; Immunofluorescence; Western Blot etc. no "Furthermore, measurement of?SOX9?transcript levels revealed a significant increase in the total lung transcripts of?SOX9?in individuals with IPF compared with those in healthy controls." 34520400 Dysregulated overexpression of Sox9 induces fibroblast activation in pulmonary fibrosis 2021 lung idiopathic_pulmonary_fibrosis homo_sapiens EIF4EBP1 1978 Gene mRNA up-regulation NA mTOR pathway Western Blot; qRT-PCR; Immunofluorescence etc. yes "The analysis showed that the transcript levels of genes in the mTOR pathway, including?EIF4EBP1, MAP1LC3A?and?RPS6,?were positively correlated with fibrotic lesions. Interestingly, the transcript levels of the autophagy gene?ATG5, which is negatively regulated by mTOR, were negatively correlated with IPF." 35159160 Niclosamide Ethanolamine Salt Alleviates Idiopathic Pulmonary Fibrosis by Modulating the PI3K-mTORC1 Pathway 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens MAP1LC3A 84557 Gene mRNA up-regulation NA mTOR pathway Western Blot; qRT-PCR; Immunofluorescence etc. yes "The analysis showed that the transcript levels of genes in the mTOR pathway, including?EIF4EBP1, MAP1LC3A?and?RPS6,?were positively correlated with fibrotic lesions. Interestingly, the transcript levels of the autophagy gene?ATG5, which is negatively regulated by mTOR, were negatively correlated with IPF." 35159160 Niclosamide Ethanolamine Salt Alleviates Idiopathic Pulmonary Fibrosis by Modulating the PI3K-mTORC1 Pathway 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens RPS6 6194 Gene mRNA up-regulation NA mTOR pathway Western Blot; qRT-PCR; Immunofluorescence etc. yes "The analysis showed that the transcript levels of genes in the mTOR pathway, including?EIF4EBP1, MAP1LC3A?and?RPS6,?were positively correlated with fibrotic lesions. Interestingly, the transcript levels of the autophagy gene?ATG5, which is negatively regulated by mTOR, were negatively correlated with IPF." 35159160 Niclosamide Ethanolamine Salt Alleviates Idiopathic Pulmonary Fibrosis by Modulating the PI3K-mTORC1 Pathway 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens ATG5 9474 Gene mRNA down-regulation NA mTOR pathway Western Blot; qRT-PCR; Immunofluorescence etc. yes "The analysis showed that the transcript levels of genes in the mTOR pathway, including?EIF4EBP1, MAP1LC3A?and?RPS6,?were positively correlated with fibrotic lesions. Interestingly, the transcript levels of the autophagy gene?ATG5, which is negatively regulated by mTOR, were negatively correlated with IPF." 35159160 Niclosamide Ethanolamine Salt Alleviates Idiopathic Pulmonary Fibrosis by Modulating the PI3K-mTORC1 Pathway 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens CHIT1 1118 Gene mRNA up-regulation NA NA Chitotriosidase Assay; YKL-40 Assay etc. yes "This explorative study findings add further evidence that CHIT1 and YKL-40 are upregulated in patients with IPF, and suggest that longitudinally stable serum CHIT1 activity and YKL-40 concentration levels may potentially be associated with the antifibrotic treatment response." 35222369 Longitudinal and Comparative Measures of Serum Chitotriosidase and YKL-40 in Patients With Idiopathic Pulmonary Fibrosis 2022 lung idiopathic_pulmonary_fibrosis homo_sapiens CHI3L1 1116 Gene mRNA up-regulation NA NA Chitotriosidase Assay; YKL-40 Assay etc. yes "This explorative study findings add further evidence that CHIT1 and YKL-40 are upregulated in patients with IPF, and suggest that longitudinally stable serum CHIT1 activity and YKL-40 concentration levels may potentially be associated with the antifibrotic treatment response." 35222369 Longitudinal and Comparative Measures of Serum Chitotriosidase and YKL-40 in Patients With Idiopathic Pulmonary Fibrosis 2022 heart myocardial_infarction homo_sapiens KLF5 688 Gene mRNA down-regulation mir-27a TGF-BETA SIGNALING PATHWAY bioinformatic analyses;luciferase assays no KLF5 possibly induces cell and tissue damage in myocardial infarction through downregulation of miR-27a and the subsequent activation of GFPT2/TGF-beta/Smad2/3 axis. 33910455 Promoting roles of KLF5 in myocardial infarction in mice involving microRNA-27a suppression and the following GFPT2/TGF-beta/Smad2/3 axis activation 2021 heart diabetic_cardiomyopathy homo_sapiens KLK8 11202 Gene mRNA up-regulation NA TGF-BETA SIGNALING PATHWAY NA no "KLK8 overexpression led to plakoglobin-dependent association of p53 with hypoxia inducible factor (HIF)-1alpha, which further enhanced the transactivation effect of HIF-1alpha on the TGF-beta1 promoter. KLK8 also induced the binding of p53 with Smad3, subsequently promoting pro-EndMT reprogramming via the TGF-beta1/Smad signaling pathway in human coronary artery endothelial cells." 33754057 A novel role of kallikrein-related peptidase 8 in the pathogenesis of diabetic cardiac fibrosis 2021 heart endomyocardial_fibrosis homo_sapiens E2F1 1869 Gene mRNA up-regulation CCNE2 NA luciferase report assay;immunoprecipitation no "E2F1 and its downstream target gene CCNE2 play a vital role in TGF-beta1-induced HCFs differentiation, thus E2F1 and CCNE2 may be a potential therapeutic target for cardiac fibrosis." 34521301 E2F transcription factor 1 (E2F1) promotes the transforming growth factor TGF-beta1 induced human cardiac fibroblasts differentiation through promoting the transcription of CCNE2 gene 2021 kidney nephrolithiasis homo_sapiens CXCR4 7852 Gene mRNA up-regulation NA NF-KAPPA B SIGNALING PATHWAY RNA sequencing;qRT-PCR;immunohistochemistry etc. no CXCR4 inhibition attenuates CaOx crystal deposition-induced renal fibrosis by suppressing autophagy and EMT through the NF-kB pathway. 35255299 CXCR4 inhibition attenuates calcium oxalate crystal deposition-induced renal fibrosis 2022 kidney chronic_kidney_disease homo_sapiens LMCD1 2995 Gene mRNA up-regulation NA NA NA no Inhibition of LMCD1 protects against renal interstitial fibrosis by impeding ERK activation. 34968577 Suppression of LMCD1 ameliorates renal fibrosis by blocking the activation of ERK pathway 2022