Tracking significant modules and key genes for esophageal squamous cell carcinoma based on differential modules.

Abstract

The exact molecular mechanism of esophageal squamous cell carcinoma (ESCC) is still unknown, and the prognosis of ESCC has not been significantly improved. To understand the molecular mechanism of ESCC, differential modules (DMs) and key genes were identified through conducting analysis on the differential co-expression network (DCN) based on the gene expression profiles of ESCC and protein-protein interaction (PPI) data. First, gene expression profiles of ESCC and PPI data recruiting and preprocessing were conducted; then, a DCN was constructed based on the gene co-expression and gene differential expression in ESCC; in the following, candidate DMs were mined from DCN through a systemic module searching strategy, and significance analysis was performed on candidate DMs to identify DMs; moreover, significant genes contained in the DMs were analyzed to identify the underlying biomarkers for ESCC. Finally, pathway enrichment analysis was conducted to disclose the function of these DMs. A total of 10,975 genes were obtained after comprehensively preprocessing on the gene expression profiles and PPI data. Then, a DCN with 915 nodes (1164 interactions) was built, and 45 seed genes were identified. In the following, four DMs that separately enriched in phenylalanine metabolism, nicotine addiction, phenylalanine metabolism, and B-cell receptor signaling pathway were identified, where module 1 and module 3 were all enriched in phenylalanine metabolism pathway. Furthermore, the most significant seed gene myeloperoxidase (MPO) was contained in all of the DMs. In this study, we successfully identified 4 DMs, three significant pathways, and a key gene MPO in ESCC, which might play key roles during the occurrence and development of ESCC and could be chosen as good indicators and therapeutic schedule for ESCC.