Multiscale Embedded Gene Co-expression Network Analysis
Fig 6
Comparison of MEGENA (as a combination of the multiscale clustering analysis and PFN) and various combinations of the established clustering techniques (eigenvector, infomap, walktrap, WGCNA) and the networks (PFN, FDRN, WGCN) using the TCGA BRCA gene expression data.
Two different similarity measures (MI and PCC) were used to perform analyses to compare robustness with respect to difference in measures to evaluate interactions. A) The number of significantly enriched functional/pathway signatures (Bonferroni corrected FET p-values) from MSigDB at various p-value thresholds against. B) Number of significantly enriched functional/pathway signatures from MSigDB at the various odds ratio thresholds. C) Number of clusters predictive of patient survival (based on FDR corrected Cox p-values) at various significance levels. D) Number of clusters predictive of patient survival (based on FDR corrected Cox p-values) and associated to at least one significantly under-represented signatures with Bonferroni corrected FET p-value < 0.05.