Identifying colon cancer stage related genes and their cellular pathways

Bolin Chen; Nandita Chakrobortty; Apu Kumar Saha; Xuequn Shang

doi:10.3389/fgene.2023.1120185

Identifying colon cancer stage related genes and their cellular pathways

Front Genet. 2023 Jan 19:14:1120185. doi: 10.3389/fgene.2023.1120185. eCollection 2023.

Authors

Bolin Chen^{1

2

3}, Nandita Chakrobortty¹, Apu Kumar Saha¹, Xuequn Shang^{1

2

3}

Affiliations

¹ School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
² MIIT Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University, Xi'an, Shaanxi, China.
³ National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, Northwestern Polytechnical University, Xi'an, Shaanxi, China.

Abstract

In the world, colon cancer is regarded as one of the most common deadly cancer. Due to the lack of a better understanding of its prognosis system, this prevailing cancer has the second-highest morbidity and mortality rate compared with other cancers. A variety of genes are responsible to participate in colon cancer and the molecular mechanism is almost unsure. In addition, various studies have been done to identify the differentially expressed genes to investigate the dysfunctions of the genes but most of them did it individually. In this study, we constructed a functional interaction network for identifying the group of genes that conduct cellular functions and Protein-Protein Interaction network, which aims to better understanding protein functions and their biological relationships. A functional evolution network was also generated to analyze the dysfunctions from initial stage to later stage of colon cancer by investigating the gene modules and their molecular functions. The results show that the proposed evolution network is able to detect the significant cellular functions, which can be used to explore the evolution process of colon cancer. Moreover, a total of 10 core genes associated with colon cancer were identified, which were INS, SNAP25, GRIA2, SST, GCG, PVALB, SLC17A7, SLC32A1, SLC17A6, and NPY, respectively. The responsible candidate genes and corresponding pathways presented in this study could be used to develop new tumor indicators and novel therapeutic targets for the prevention and treatment of colon cancer.

Keywords: cancer evolution; cancer stage; colon cancer; differentially expressed gene; functional evolution network.

Grants and funding

This work was supported by the National Natural Science Foundation of China under Grant No. 61972320 and the National Key R&D Program of China (No. 2021YFA1000400).