The integrative analysis of protein–protein interactions and co-regulated 5hmC modules highlighted cancer relevant genes as the network hubs (Fig. 3H, I, Additional file 2: Fig. S2D-F), including CCDC125 (encoding coiled-coil domain containing 125) in module M1 (Fig. 3H) and CTNNA3 (encoding catenin alpha 3) in module M3 (Fig. 3I), distinct from what was observed from the mRNA–5hmC co-regulation analysis. The gene discussed is CCDC125; the disease is cancer.