Identification of key genes in colorectal cancer using random walk with restart.

Abstract

As the most common type of cancer and the second leading cause of cancer-associated mortality, colorectal cancer (CRC) has received increasing attention. The aim of the present study was to investigate the mechanisms of CRC by analyzing the microarray dataset, GSE32323. The GSE32323 dataset was downloaded from the Gene Expression Omnibus, and included 17pairs of matched cancer and normal colorectal tissue samples. The differentially expressed genes (DEGs) were screened using the Linear Models for Microarray Data package and a search of CRC genes, also denoted as seed genes, was performed using the Online Mendelian Inheritance in Man database. Subsequently, the protein‑protein interaction (PPI) network was downloaded from the Search Tool for the Retrieval of Interacting Genes database and the sub‑network (CRC.PPI) of the DEGs and seed genes were obtained. In addition, the top 50nodes with highest affinity scores in the CRC.PPI were identified using random walk with restart analysis. The potential functions of the DEGs included in the top 50nodes were analyzed using the Database for Annotation, Visualization and Integrated Discovery online tool. Using the Drug Gene Interaction database, drug‑gene interaction analysis was performed to identify antineoplastic drug interacts with genes. A total of 1,640DEGs between the CRC and normal samples were screened. The obtained seed genes included cyclinD1 (CCND1) and aurora kinase A (AURKA). The enriched functions for the 31DEGs in the PPI network of the top 50nodes were predominantly associated with cell cycle. The DEGs may function in CRC by interacting with other genes in the PPI network of the top 50nodes, for example, DEP domain‑containing MTOR‑interacting protein (DEPTOR)‑CCND1, AURKA‑breast carcinoma amplified sequence‑1 (BCAS1), CCND1‑BCAS1, CCND1‑neural precursor cell expressed developmentally downregulated9 (NEDD9) and CCND1‑mitogen‑activated protein kinase kinase2 (MAP2K2). Only three DEGs (CCND1, AURKA and DEPTOR) had interactions with their corresponding antineoplastic drugs. Taken together, DEPTOR,AURKA,CCND1, BCAS1,NEDD9 and MAP2K2 may act in CRC.