Probing pathway-related modules in invasive squamous cervical cancer based on topological centrality of network strategy

Abstract

Objective: Our work aimed to identify pathway-related modules and hub genes involved in invasive squamous cervical cancer (SCC) based on topological centralities analysis of networks. Materials and Methods: To determine the functional modules changed in SCC, functional enrichment analyses were performed for differentially expressed genes (DEGs) between invasive SCC samples and normal controls. Then, co-expression network was constructed using EBcoexpress approach based on the DEGs. Moreover, pathway-related modules were probed from the global co-expression network based on pathway genes and their adjacent genes. Finally, topological centralities for co-expression network and pathway-related subnetworks were carried out to explore hub genes and significant pathway-related functional modules. Results: Functional analyses revealed that DEGs mainly involved in three biological processes (metabolic process, cellular process, and cellular component organization) and 8 significant pathways. Furthermore, the co-expression network with 659 nodes and 1087 edges and 8 pathway-related modules were obtained. Topological centralities indicated two significant modules (cell cycle and base excision repair pathway-related modules), in which the common hub gene ARFGAP3 showed the most significant importance. Conclusions: The bioinformatics elucidation of certain pathway-related modules and hub genes might be beneficial to understand the molecular pathogenesis and reveal their potential as novel molecular markers of SCC to a great extent.