The work flow of dysfunctional methylation, microRNA and mRNA gene set analysis.

<p>First, for each Gene Ontology (GO) term, we defined three gene sets: the methylation set, the microRNA set and the mRNA set. Next, we calculated the Matthews's correlation coefficient (MCC), as evaluated by leave-one-out cross-validation (LOOCV), for each gene set. Next, we ranked the MCCs in the methylation sets, the microRNA sets and the mRNA sets, and we compared the MCC ranks of methylation, microRNA and mRNA for each Gene Ontology (GO) term and classified the GO sets into six groups. Finally, we identified the dysfunctional methylation, microRNA and mRNA gene sets in lung cancer.