Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types

Prognostic genes are key molecules informative for cancer prognosis and treatment. Previous studies have focused on the properties of individual prognostic genes, but have lacked a global view of their system-level properties. Here we examined their properties in gene co-expression networks for four cancer types using data from The Cancer Genome Atlas. We found that prognostic mRNA genes tend not to be hub genes (genes with an extremely high connectivity), and this pattern is unique to the corresponding cancer-type specific network. In contrast, the prognostic genes are enriched in modules (., a group of highly interconnected genes), especially in module genes conserved across different cancer co-expression networks. The target genes of prognostic miRNA genes show similar patterns. We identified the modules enriched in various prognostic genes, some of which show cross-tumor conservation. Given the cancer types surveyed, our study presents a view of emergent properties of prognostic genes.