title: 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 17 pairs 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 50 nodes 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 50 nodes 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 1,640 DEGs between the CRC and normal samples were screened. The obtained seed genes included cyclin D1 (CCND1) and aurora kinase A (AURKA). The enriched functions for the 31 DEGs in the PPI network of the top 50 nodes were predominantly associated with cell cycle. The DEGs may function in CRC by interacting with other genes in the PPI network of the top 50 nodes, 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 downregulated 9 (NEDD9) and CCND1‑mitogen‑activated protein kinase kinase 2 (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.
authors.affiliation: Department of Gastrointestinal Colorectal and Anal Surgery, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Cui
authors.affiliation: Department of Gastrointestinal Colorectal and Anal Surgery, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Kexin
authors.initials: K
authors.lastname: Shen
authors.affiliation: Department of Gastrointestinal Colorectal and Anal Surgery, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Zhongshi
authors.initials: Z
authors.lastname: Xie
authors.affiliation: Department of General Surgery, Jilin University, Changchun, Jilin 130022, P.R. China.
authors.forename: Tongjun
authors.initials: T
authors.lastname: Liu
authors.affiliation: Department of Gastrointestinal Colorectal and Anal Surgery, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China.
authors.forename: Haishan
authors.initials: H
authors.lastname: Zhang
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D003106:Colon / Q000187:drug effects / Q000378:metabolism / Q000473:pathology; D015179:Colorectal Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D063990:Gene Ontology; D006801:Humans; D060066:Protein Interaction Maps / Q000187:drug effects; D012007:Rectum / Q000187:drug effects / Q000378:metabolism / Q000473:pathology
chemical_list: D000970:Antineoplastic Agents