Identification of disrupted pathways associated with colon cancer based on combining protein-protein interactions and pathway data

Abstract

Objective: The objective of this paper was to identify the disrupted pathways associated with colon cancer at a network level based on protein-protein interaction (PPI) network and pathway analysis. Materials and Methods: First of all, the Affymetrix microarray data of colon cancer, human PPIs relationships, and human pathways existed in the database were recruited and preprocessed. Second, differentially expressed genes (DEGs) between colon cancer and normal controls were identified. In the following, an objective PPI network was constructed using these DEGs. Ultimately, we calculated the disrupted pathways based on the intersection between pathway network and the objective network. Meanwhile, the topological centrality (degree) analysis was performed to explore the hub genes in the objective network. Results: In our study, an objective network consisted of 2288 PPI pairs by 574 DEGs were constructed. In addition, ten disrupted pathways whose number of intersection was not <22 between objective network and each pathway, as well as P < 0.05, was selected. Furthermore, a total of 22 hub genes in the objective network were selected based on degree >30. Last, seven out of the above ten pathways were validated to involve in the intersections of pathway network and objective network. Moreover, cell cycle was the most significant disrupted pathway. Conclusions: We successfully identified several biologically disrupted pathways, and these pathways might be potential biomarkers in detection and treatment for colon cancer.