Identification of key modules and hub genes associated with lung function in idiopathic pulmonary fibrosis

PeerJ
Yuechong XiaHong Luo

Abstract

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease, characterized by a decline in lung function. To date, the pathophysiologic mechanisms associated with lung dysfunction remain unclear, and no effective therapy has been identified to improve lung function. In the present study, we used weighted gene co-expression network analysis (WGCNA) to identify key modules and hub genes associated with lung function in IPF. Three datasets, containing clinical information, were downloaded from Gene Expression Omnibus. WGCNA was performed on the GSE32537 dataset. Differentially expressed gene s (DEGs) between IPF patients and healthy controls were also identified to filter hub genes. The relationship between hub genes and lung function was then validated using the GSE47460 and GSE24206 datasets. The red module, containing 267 genes, was positively correlated with the St. George's Respiratory Questionnaire score (r = 0.37, p < 0.001) and negatively correlated with the percent predicted forced vital capacity (FVC% predicted) (r =  - 0.46, p < 0.001) and the percent predicted diffusion capacity of the lung for carbon monoxide (Dlco% predicted) (r =  - 0.42, p < 0.001). Gene Ontology and Kyoto Encyclopedi...Continue Reading

References

Jun 1, 1996·Clinical Immunology and Immunopathology·I ShaharS Ben Efraim
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Fengrong ZuoRenu A Heller
Apr 26, 2003·American Journal of Respiratory Cell and Molecular Biology·Yuben P MoodleyDarryl A Knight
May 20, 2003·Nature Immunology·Hideo YasukawaAkihiko Yoshimura
Nov 26, 2003·Nature Immunology·Masato KuboAkihiko Yoshimura
Jan 9, 2004·The New England Journal of Medicine·Ganesh RaghuUNKNOWN Idiopathic Pulmonary Fibrosis Study Group
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Bin Zhang, Steve Horvath
Sep 26, 2006·American Journal of Respiratory and Critical Care Medicine·Ivana V YangDavid A Schwartz
Jul 7, 2007·Expert Opinion on Therapeutic Targets·Hongwei Gao, Peter A Ward
Aug 2, 2008·American Journal of Respiratory and Critical Care Medicine·Ganesh RaghuSaeed Fatenejad
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Apr 14, 2009·American Journal of Respiratory and Critical Care Medicine·Kazuhisa KonishiNaftali Kaminski
Jun 25, 2009·Current Opinion in Pulmonary Medicine·Stephen K Frankel, Marvin I Schwarz
Mar 24, 2010·Journal of Biopharmaceutical Statistics·Wei ZhaoSteve Hovarth
Apr 8, 2011·American Journal of Respiratory and Critical Care Medicine·Ganesh RaghuUNKNOWN ATS/ERS/JRS/ALAT Committee on Idiopathic Pulmonary Fibrosis
Jul 6, 2011·The Journal of Experimental Medicine·Thomas A Wynn
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Jul 23, 2013·The Journal of Immunology : Official Journal of the American Association of Immunologists·Jianmin XueSteven R Duncan
May 20, 2014·The New England Journal of Medicine·Luca RicheldiUNKNOWN INPULSIS Trial Investigators
Sep 2, 2014·BMC Bioinformatics·Philippe BardouChristophe Klopp
Dec 3, 2014·The American Journal of Pathology·Amarnath Satheesh MarudamuthuSreerama Shetty
Feb 5, 2015·Genome Research·Helen SpiersJonathan Mill
Mar 3, 2015·Respiratory Medicine·Hyun Joo KimRade Tomic
Nov 22, 2015·BMC Pulmonary Medicine·Yong HuangImre Noth
May 4, 2016·Cellular and Molecular Life Sciences : CMLS·R MahonyN J Stevenson
Apr 4, 2017·Lancet·Luca RicheldiMark G Jones
Aug 8, 2017·Annals of Anatomy = Anatomischer Anzeiger : Official Organ of the Anatomische Gesellschaft·Basma Emad Aboulhoda
Sep 13, 2017·Respiration; International Review of Thoracic Diseases·Ulrich CostabelPaul W Noble
Oct 21, 2017·Nature Reviews. Disease Primers·Fernando J MartinezAthol U Wells
May 10, 2018·The New England Journal of Medicine·David J Lederer, Fernando J Martinez
Feb 2, 2019·Respiratory Medicine·P HeukelsM Kool
Mar 15, 2019·Respiratory Research·Ulrich CostabelPaul W Noble
Oct 23, 2019·Journal of Cellular Physiology·Xinghua MengJianhua Xiao

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Datasets Mentioned

BETA
GSE32537
GSE47460
GSE24206
GES32537

Methods Mentioned

BETA
chip
biopsy

Software Mentioned

affyPLM
R package “ ggstatsplot
Cytoscape
R package “ ggpubr
R package
RobustRankAggreg
R package “ WGCNA
affy
RobustRankAggreg ( RRA )
R

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