Abstract
The purpose of this study was to identify genes related to bladder cancer with samples from normal and disease cases by microarray chip. After downloading the gene expression profile GSE3167 from Gene Expression Omnibus database which includes 50 bladder samples, comprising 9 normal and 41 disease samples, differentially expressed genes were identified with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Firstly, molecular functions, biological processes and cell component analysis were researched by software Gestalt. Then, software String was used to search interaction relationships among differentially expressed genes, and hub genes of the network were selected. Finally, by using plugins of software Cytoscape, Mcode and Bingo, module analysis of hub-genes was performed. A total of 221 genes were identified as differentially expressed by comparing normal and disease bladder samples, and a network as well as the hub gene C1QBP was obtained from the network. The C1QBP module had the closest relationship to production of molecular mediators involved in inflammatory responses. We obtained differentially expressed genes of bladder cancer by microarray, and both PRDX2 and YWHAZ in the module with hub gene C1QBP were most significantly related to production of molecular mediators involved in inflammatory responses. From knowledge of inflammatory responses and cancer, our results showed that, the hub gene and its module could induce inflammation in bladder cancer. These related genes are candidate bio-markers for bladder cancer diagnosis and might be helpful in designing novel therapies.
Highlights
Bladder cancer (BC) is estimated to be the ninth most common cause of cancer worldwide and the 13th most numerous cause of death from cancer (Parkin, 2008)
We obtained differentially expressed genes of bladder cancer by microarray, and both Peroxiredoxin 2 (PRDX2) and YWHAZ in the module with hub gene C1QBP were most significantly related to production of molecular mediators involved in inflammatory responses
Constructing protein interaction network Protein-protein interactions (PPIs) had been marked as the main actors for all of the processes taking place in Screening for differentially expressed genes The differences of normalized expression data were compared after data preprocessing (Figure 1)
Summary
Bladder cancer (BC) is estimated to be the ninth most common cause of cancer worldwide and the 13th most numerous cause of death from cancer (Parkin, 2008). It remains the fifth leading new cancer diagnosis in the United States (US), the fourth most common malignancy in men and the ninth most common in women in the US (Siegel et al, 2008). There are more alterations in the receptor tyrosine kinase–Ras pathway, especially the mutation of HA-RAS (HRAS) and fibroblast growth factor receptor 3 (FGFR3) genes in low-grade non-invasive BC than normal tissue (Pasin et al, 2008). Numerous factors within the mTORsignaling cascade have appear to be altered in BC (Chingand Hansel, 2010)
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