Evaluation of clustering performance using MCL at various I values was determined by calculating the fraction of modules enriched with one annotation at FDR < 0.05 (expressed as specificity) and the fraction of annotations enriched in at least one module at FDR < 0.05 (expressed as sensitivity), having at least 2 genes associated with the enriched annotation [ 59].
Indeed, we found that when comparing the fraction of the module that corresponded to the known KEGG pathway, DEGAS consistently outperformed jActiveModules, and performed better than all the competing methods in six datasets (Figure 3C).
Columns list the module label, module size, rank of the enrichment p-value for that particular module, the Bonferroni-corrected enrichment p-value (the correction is performed with respect to the number of GO terms), fraction of the module genes also in the GO term, GO ontology, and GO term name.
Hence, the large fraction of significant modules indicates that our division into modules based on common motifs and co-expression is indeed relevant.
The significance P-value was the fraction of these modules in 1000.
For each network we evaluated two measures: functionality, defined as the fraction of structural modules that were significantly enriched for a metabolic function, and coverage – the fraction of biological functions that could be mapped to structural modules.
The Best-Neighbors variant performs slightly better than All-Neighbors in terms of the fraction of enriched modules, but All-Neighbors performs significantly better in terms of category coverage, due to its inclusion of back nodes.
As said, the optimization function is defined to be zero in one case, when the fraction of within-module links is equal to what we would expect for a randomized network of equivalent size.
Finally, we calculated the fraction (r) of modules that can not be characterized by the global network parameters.
As mentioned earlier, the basic idea is to test whether the proportion of the module genes in the signature of size n i is significantly larger than the "population -fraction of the module genes in the expopulation -fractionze N i.
