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Series GSE28221 Query DataSets for GSE28221
Status Public on Oct 15, 2013
Title Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Background: In this study we aimed to identify peripheral blood mononuclear cell (PBMC) gene expression profiles predictive of poor outcomes in idiopathic pulmonary fibrosis (IPF)
Methods: Microarray analyses of PBMC were performed in 120 patients from discovery (n=45) and replication cohorts (n=75). Genes and pathways associated with transplant-free survival (TFS) were identified and confirmed by qRT-PCR.
Findings: 52 genes were predictive of TFS in a discovery cohort (FDR<5%, Cox score above 2.5 or below -2.5). Clustering the replication cohort samples using these genes distinguished two patient groups with significantly different TFS (hazard ratio 1.96, 95%CI 1.01-3.8, P=0.018). Decreased expression of “The co-stimulatory signaling during T cell activation” Biocarta pathway and in particular CD28, ICOS, LCK and ITK was associated with shorter TFS times in each cohort (FDR<5%). qRT-PCR expression of CD28, ICOS, LCK and ITK correlated with the microarray results in the discovery cohort (P<0.05) and their decreased expression was predictive of shorter TFS in the replication cohort (P<0.05). A genomic and clinical model demonstrated an area under the ROC curve of 78.5% at 2.4 months for death and lung transplant prediction.
Interpretation: Our results suggest that CD28, ICOS, LCK and ITK are outcome biomarkers in IPF.
 
Overall design The 'GeneID_matched_gene_expression_dataset_of_IPF_cohorts.txt' supplementary data file contains the matched gene expression data of the subseries GSE28042 with the subseries GSE27957 by gene ID (details in the readme.txt)

This SuperSeries is composed of the SubSeries listed below.
 
Citation(s) 24089408, 26589497
Submission date Mar 28, 2011
Last update date Mar 30, 2020
Contact name JOSE DAVID HERAZO MAYA
Organization name Yale University
Department Medicine
Lab Kaminski Lab
Street address 300 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (2)
GPL5175 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Samples (139)
GSM691362 PBMC expression profile of IPF patient_P34
GSM691363 PBMC expression profile of IPF patient_P35
GSM691364 PBMC expression profile of IPF patient_P36
This SuperSeries is composed of the following SubSeries:
GSE27957 Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis [Affymetrix]
GSE28042 Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis [Agilent]
Relations
BioProject PRJNA139675

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE28221_GeneID_matched_gene_expression_dataset_of_IPF_cohorts.txt.gz 10.9 Mb (ftp)(http) TXT
GSE28221_RAW.tar 1.2 Gb (http)(custom) TAR (of CEL, TXT)
GSE28221_readme.txt 28.6 Kb (ftp)(http) TXT

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