Weighted gene co-expression network analysis identified MYL9 and CNN1 are associated with recurrence in colorectal cancer

Journal of Cancer
Xiao QiuXin-You Zhang

Abstract

Colorectal cancer (CRC) is one of the most common carcinomas and the fourth leading cause of cancer-related death worldwide. One of the obstacles in the successful treatment of CRC is a high rate of recurrence. We aimed to construct weighted gene co-expression network analysis (WGCNA) to identify key modules and hub genes in association with recurrence in CRC patients. We firstly used the microarray data, GSE41258, to construct a co-expression network and identify gene modules. Furthermore, protein and protein interaction (PPI) network was also performed to screen hub genes. To validate the hub genes, an independent dataset GSE17536 was used for survival analyses. Additionally, another two databases were also performed to investigate the survival rates and expression levels of hub genes. Gene set enrichment analyses (GSEA) combined with gene ontology (GO) were performed to further explore function and mechanisms. In our study, the midnightblue module was identified to be significant, 15 hub genes were screened, four of which were identified as hub nodes in the PPI network. In the test dataset, we found higher expression of MYL9 and CNN1 were significantly associated with shorter survival time of CRC patients. GO analyses showed...Continue Reading

Datasets Mentioned

BETA
GSE17536
GSM1012533
GSM1012326
GSM1012604
GSE41258

Methods Mentioned

BETA
PCR

Software Mentioned

GSEA
WGCNA
R package
Search Tool for the Retrieval
simpleaffy
GEPIA
affy
affyPLM
anRichment
R

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