Bioinformatic Identification of Hub Genes and Analysis of Prognostic Values in Colorectal Cancer

Abstract

The purpose of this study is to discover novel hub genes which are helpful for diagnosis, prognosis, and targeted therapy in colorectal cancer (CRC) by using bioinformatics analysis. GSE74602, GSE110225, and GSE113513 were extracted from the gene expression omnibus (GEO). Differentially expressed genes (DEGs) in expression profiles were identified by GEO2R. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the DEGs were carried out in the Database for Annotation, Visualization, and Integrated Discovery (DAVID). String database and cytoscape were used for building protein–protein interaction (PPI) network and module analysis. The UALCAN was used for in-depth analysis of data of CRC patients from The Cancer Genome Atlas (TCGA) to identify expression levels and overall survival rates of hub genes. The DEGs included 107 up-regulation genes and 232 down-regulation genes. Twenty-nine (29) hub genes and two significant modules were screened from PPI network. The expression levels of hub genes in TCGA were verified. Survival analysis curve indicated high expression of CCNA2, CCNB1, DLGAP5, were related to high survival rates, and low expression of TIMP1 were associated with high survival rates. These results suggest that DEGs may be the hub genes of CRC, and CCNA2, CCNB1, DLGAP5, TIMP1 may be the potential prognostic markers of CRC.

Acknowledgments

We would like to thank Ting Luo (Jinan University Guangzhou) for the help in reviewing and editing this paper. Lei Li (Guangdong University of Technology) edited the English version of the final manuscript.

Disclosure Statement

The authors declare that they have no conflict of interest.

Ethical Approval

There are no animals and human experiments involved in this study.

Availability of Data and Materials

The datasets used and analyzed in research are available from the corresponding author on reasonable request (GEO, https://www.ncbi.nlm.nih.gov/geo/).

Funding

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors. The authors declare that they have no conflict of interest.

Author Contributions

Xinyi Lei and Zhiyong Dong performed the study and wrote the manuscript. Cunchuan Wang conceived and designed the study. Zhiyong Dong, Jing Jing, Miao Zhang and Bingsheng Guan revised and edited the manuscript. All authors read and approved this manuscript. All authors agreed to take responsibility and be accountable for the contents of the article and to share responsibility to answer any questions raised about the accuracy or integrity of the published work.