Comprehensive network analysis of genes expressed in human oropharyngeal cancer.

PURPOSE: Oropharyngeal cancer (OPC) is the eighth most common cancer worldwide, however the genes involved in the development of OPC have been reported few. We constructed a co-expression network to extend knowledge of the molecular biomarkers in OPC development.

MATERIALS AND

METHODS

Microarray data of HPV-active, -inactive, -negative OPC and normal benign tissue (uvula, tonsil) (Series GSE55550) were retrieved from NCBI GEO DataSets. We performed co-expression analysis of OPC transcriptome data by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off using 13 guide genes.

RESULTS

The OPC subnetwork contained three clusters: cell cycle (62 node genes and 125 edge genes), immune system (44 node genes and 70 edge genes) and organ morphogenesis (128 node gene and 215 edge genes) process separately.

CONCLUSION

Our co-expression analysis includes separated transcriptomes of OPC, which is a useful resource for OPC researchers to elucidate important and complex biological events, to prevent and to predict cancer.