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Series GSE24206 Query DataSets for GSE24206
Status Public on Nov 01, 2011
Title Validated Gene Expression Signatures of Idiopathic Pulmonary Fibrosis
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Idiopathic pulmonary fibrosis (IPF) is a chronic fibrosing lung disease that is difficult to diagnose and follows an unpredictable clinical course. The object of this study was to develop a predictive gene signature model of IPF from whole lung tissue. We collected whole lung samples from 11 IPF patients undergoing diagnostic surgical biopsy or transplantation. Whenever possible, samples were obtained from different lobes. Normals consisted of healthy organs donated for transplantation. We measured gene expression on microarrays. Data were analyzed by hierarchical clustering and Principal Component Analysis. By this approach, we found that gene expression was similar in the upper and lower lobes of individuals with IPF. We also found that biopsied and explanted specimens contained different patterns of gene expression; therefore, we analyzed biopsies and explants separately. Signatures were derived by fitting top genes to a Bayesian probit regression model. We developed a 153-gene signature that discriminates IPF biopsies from normal. We also developed a 70-gene signature that discriminates IPF explants from normal. Both signatures were validated on an independent cohort. The IPF Biopsy signature correctly diagnosed 76% of the validation cases (p < 0.01), while IPF Explant correctly diagnosed 78% (p < 0.001). Examination of differentially expressed genes revealed partial overlap between IPF Biopsy and IPF Explant and almost no overlap with previously reported IPF gene lists. However, several overlapping genes may provide a basis for developing therapeutic targets.
 
Overall design 17 samples from 11 patients with IPF (6 patients provided a pair of samples from upper and lower lobes; 5 patients contributed singleton samples); 6 control specimens were obtained from routine lung volume reduction of healthy donor lungs at the time of lung transplantation.
 
Contributor(s) Meltzer E
Citation(s) 21974901
Submission date Sep 17, 2010
Last update date Mar 25, 2019
Contact name Eric B. Meltzer
E-mail(s) eric.meltzer@duke.edu
Phone 919-681-5961
Fax 919-681-4637
Organization name Duke University
Department Department of Medicine, Division of Pulmonary, Allergy and Critical Care
Street address DUMC 102355
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (23)
GSM595407 Healthy donor_biological replicate1
GSM595411 Healthy donor_biological replicate2
GSM595414 Healthy donor_biological replicate3
Relations
BioProject PRJNA130183

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Supplementary file Size Download File type/resource
GSE24206_RAW.tar 109.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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