Comparison between pathway enrichment studies for differential expression and differential connectivity.

<p>(<b>A-E</b>) Benjamini–Hochberg False Discovery Rate (FDR) as a function of the p-value. Red color refers to the pathways enriched of differentially expressed genes (DE). Blu color refers to the pathways enriched of differentially expressed genes or differentially connected ones (DEC). (<b>F</b>) Reactome pathways of Immune System. Enrichment meta-analysis p-values across the tissues for ``Reactome Immune System'', its first and second sub-pathways. The histogram in the inset shows the tissue-specific enrichment p-values of ``Reactome Immune System''. (<b>G-H</b>) Core set pathway enrichment analysis. The numbers of core set pathways found as significant at 0.01 level (<b>G</b>) and in the top-ranked positions (<b>H</b>) are displayed on the bars. In the inset it is reported the p-value associated to the relative merit of DEC measure with respect to DE obtained by a permutation test.