Fig. 5

Performance benchmarking on TCGA data. a Percentage of negatively and positively correlated modules, where green denotes a positive correlation and blue for negative correlation, (b) Distribution of absolute values of module correlation between methylation and expression, where p-values are computed using the student t-test, (c) Specificity of the methods. Gene modules found by each method are evaluated by a set of gold-standard pathway annotation. Specificity is defined as the fraction of gene modules significantly enriched for genes of some reference sets, and (d) Sensitivity of the methods. Sensitivity is defined as the fraction of reference sets significantly enriched for genes of some modules. Enrichment p-values are computed using hypergeometric test and corrected by Benjamin-Hochberg, where * denotes p<0.05