Open AccessA Pipeline to Call Multilevel Expression Changes between Cancer and Normal Tissues and Its Applications in Repurposing Drugs Effective for Gastric Cancer
Author(s) -
Wei Gao,
Jun Yang,
Changhua Zhuo,
Sha Huang,
Lin Jia,
Guangfeng Wu,
Min Zhou
Publication year - 2020
Publication title -
biomed research international
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.772
H-Index - 126
eISSN - 2314-6141
pISSN - 2314-6133
DOI - 10.1155/2020/3451610
Subject(s) - cancer , drug repositioning , biology , gene , cancer research , repurposing , gene expression , cancer cell , computational biology , genetics , pharmacology , ecology , drug
Differential gene analyses on gastric cancer usually focus on expression change of single genes between tumor and adjacent normal tissues. However, besides changes on single genes, there are also coexpression and expression network module changes during the development of gastric cancer. In this study, we proposed a pipeline to investigate various levels of changes between gastric cancer and adjacent normal tissues, which were used to repurpose potential drugs for treating gastric cancer. Specifically, we performed a series of analyses on 242 gastric cancer samples (33-normal, 209-cancer) downloaded from the cancer genome atlas (TCGA), including data quality control, differential gene analysis, gene coexpression network analysis, module function enrichment analysis, differential coexpression analysis, differential pathway analysis, and screening of potential therapeutic drugs. In the end, we discovered some genes and pathways that are significantly different between cancer and adjacent normal tissues (such as the interleukin-4 and interleukin-13 signaling pathway) and screened perturbed genes by 2703 drugs that have a high overlap with the identified differentially expressed genes. Our pipeline might be useful for understanding cancer pathogenesis as well as gastric cancer treatment.