Screening and further analyzing differentially expressed genes in acute idiopathic pulmonary fibrosis with DNA microarray

F. Min, F. Gao, Z. Liu

Department of Obstetrics, First People’s Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China. zhenweiliu69@163.com

 

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• Respiratory Medicine

BACKGROUND: Acute idiopathic pulmonary fibrosis (IPF) is a serious and progressive form of lung disease, and millions of people suffer from this disease in the world. To provide clues for getting a better understanding of the mechanism of this disease, we identified and further analyzed the differential expressed genes in IPF.

METHOD: In this study, we downloaded the gene expression microarray (GSE10667) from Gene Expression Omnibus (GEO) database. The dataset contained a total of 23 samples, including 15 normal controls and 8 diseases samples (IPF). Then, we identified the differentially expressed genes between normal and disease samples with packages in R language. Consequently, the PPI network was also constructed for the products of these DEGs, and modules in the network were analyzed by Cytoscape’s plug-in Mcode and Bingo. Furthermore, enrichment analysis was performed by DAVID to illustrate the altered pathways in IPF. The drug compounds for PLK1 were screened in DrugBank.

RESULTS: Atotal of 349 genes were identified as differentially expressed genes between normal and disease samples, and we constructed a protein-protein interaction network which included 200 pairs of proteins. Then three modules were identified in our network. Function of these modules were predicted to be related to protein kinase binding, extracellular matrix structural and structural constituent of cytoskeleton, respectively. Finally, we focused on module A including 18 DEGs.

CONCLUSIONS: PLK1 (Polo like kinge-1) in this module was predicted as a marker gene in IPF, which was related to cell cycle pathway. Several compounds were found which may be the potential drug for IPF.

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