Co-expression analysis reveals key gene modules and pathways of oral squamous cell carcinoma.

BACKGROUND: Oral squamous cell carcinoma is a malignant tumor which is particularly common in the developing world, mostly in older males.

OBJECTIVE: Although gene expression analyses had been performed previously, to our best knowledge, systemic co-expression analysis for this disease is still lacking to date.

METHODS: In this study, we built the co-expression modules with the help of Weighted Correlation Network Analysis (WGCNA) and investigated the function enrichment of co-expression genes from important modules by bioinformatics analysis.

RESULTS: A total of 10 co-expression modules were conducted for 4500 genes from 167 oral squamous cell carcinoma samples. Number of genes for each module ranged from 52 to 1112, with the mean of 450. Interaction relationships of hub-genes between pairwise modules showed great differences, suggesting the high confidence of modules. Functional enrichments of the co-expression modules exhibited great differences. Furthermore, genes in the module ME blue and module ME magenta significantly enriched in hsa05332 (Graft-versus-host disease) and hsa05330 (Allograft rejection), and the two pathways were associated with the oral squamous cell carcinoma.

CONCLUSION: Together, our findings provided the framework of co-expression gene modules of oral squamous cell carcinoma and further understanding of these modules at functional aspect.