Published in:
01-02-2014
RETRACTED ARTICLE: Protein–Protein Interaction Network Analysis in Chronic Obstructive Pulmonary Disease
Published in: Lung | Issue 1/2014
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Background
The aim of this study was to investigate the gene expression profile of
chronic obstructive pulmonary disease (COPD) patients and non-COPD
patients.
Methods
Microarray raw data (GSE29133) was downloaded from Gene Expression Omnibus,
including three COPD samples and three normal controls. Gene expression
profiling was performed using Affymetrix human genome u133 plus 2.0 GeneChip.
Differentially expressed genes were identified by Student’s t test and genes with p < 0.05 were considered significantly changed. Up- and
downregulated genes were submitted to the molecular signatures database (MSigDB)
to search for a possible association with other previously published gene
expression signatures. Furthermore, we constructed a COPD protein–protein
interaction (PPI) network and used the connectivity map (cMap) to query for
potential drugs for COPD.
Results
A total of 680 upregulated genes and 530 downregulated genes in COPD were
identified. The MSigDB investigation found that upregulated genes were highly
similar to gene signatures that respond to interferon and downregulated genes
were similar to erythroid progenitor cells from fetal livers of E13.5 embryos
with KLF1 knocked out. A PPI network
consisting of 814 gene/proteins and 2,613 interactions was identified by Search
Tool for the Retrieval of Interacting Genes. The cMap predicted helveticoside,
disulfiram, and lanatoside C as the top three possible drugs that could perhaps
treat COPD.
Conclusion
Comprehensive analysis of the gene expression profile for COPD versus control
reveals helveticoside, disulfiram, and lanatoside C as potential molecular
targets in COPD. This evidence provides a new breakthrough in the medical
treatment of patients with COPD.