Peer Review #1 of "Identification of 10 Hub genes related to the progression of colorectal cancer by co-expression analysis (v0.1)"

Abstract

Background Colorectal cancer (CRC) is the third most common cancer in the world. The present study is aimed at identifying Hub genes associated with the progression of CRC. Method The data of the patients with CRC were obtained from the Gene Expression Omnibus (GEO) database and assessed by weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses performed in R. by WGCNA, several hub genes that regulate the mechanism of tumorigenesis in CRC were identified. Differentially expressed genes in the data set GSE28000 and GSE42284 were used to construct a co-expression network for WGCNA. The yellow, black, and blue modules associated with CRC level were filtered. Combining the co-expression network and the PPI network, 15 candidate hub genes were screened. Results After validation using the TCGA-COAD dataset, a total of 10 Hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. The expressions of MT1G, CXCL8, IL1B, CXCL5, CXCL11 and GZMB in colorectal cancer tissues were higher than normal tissues (p-value <0.05). The expressions of MT1X, MT2A, IL10RA and KIT in colorectal cancer tissues were lower than normal tissues (p-value <0.05). Conclusions By combinating with a series of methods including GO enrichment analysis, KEGG pathway analysis, PPI network analysis and gene co-expression network analysis, we identified 10 hub genes that were associated with the progression of CRC.