Gene screening of colorectal cancers via network analysis

Abstract

Aim: Identifying crucial genes related to colorectal cancers via protein-protein interaction (PPI) network analysis is the aim of this study.

Background: colorectal cancer as major reason of mortality is evaluated by genetic and proteomic approaches to find suitable biomarkers. Chromosomal instability plays crucial role in CRC. Expression change of large numbers of genes is reported.

Methods: Differentially expressed genes related to CRCs which obtained from different proteomic methods were extracted from a review article of Paula Álvarez-Chaver et al. The genes interacted by Cytoscape software via STRING database. The central nodes determined and were enriched for biological terms by ClueGO. Action map for central genes was illustrated by CluePedia. The critical genes in CRC were introduced.

Results: Among 123 query genes, 114 one recognized by software and were included in the network. SRC, EGFR, PCNA, IL8, CTNNB1, TIMP1, CDH1, and HSPD1 were determined as central genes. After gene ontology analysis SRC, EGFR, and CDH1 were identified as critical genes related to CRC.

Conclusion: It seems that SRC, EGFR, and CDH1 and the related pathways are possible biomarkers for CRC.

Keywords: Biomarker; Colorectal cancer; Gene.

Figure 1

PPI network of colon cancer including 9 isolated nodes and a main connected component

Figure 2

Action map including activation, inhibition, and expression relative to the 8 hub-bottlenecks. Blue, green, and red colors refer to expression, activation, and inhibition actions. Kapa score is considered as default value in CluePedia

Figure 3

Biological terms relative to the 8 hub-bottlenecks. The colored terms are names of groups. Grouping p value and p value ≤ 0.05 were considered

Figure 4

Six clusters of biological term relative to the 8 central nodes are shown. Names of groups correspond to the group colors are written in the foot of figure.