Figure 4

Consistency of inferred pathway activity correlations. For each breast cancer subtype (ER+,ER-) and for the up and down transcriptional modules we compare the consistency scores of predicted Netpath pathway correlations evaluated over the 5 validation sets for the three different pathway activity estimation algorithms (UPR-AV,PR-AV,DART). The up and downregulated transcriptional modules for each pathway were inferred from Wang data set and the significant inter-pathway correlations constituted our hypotheses to be tested in the 5 validation sets. Consistency scores reflect significance as well as consistency of directionality and magnitude of correlations in the validation sets. A) Boxplot of the difference in consistency scores between PR-AV and UPR-AV methods (PR-AV minus UPR-AV). B) Boxplot of the difference in consistency scores between DART and PR-AV methods (DART minus PR-AV). C) Boxplot of the difference in consistency scores between DART and UPR-AV methods (DART minus UPR-AV). P-values are from a two-tailed paired Wilcoxon rank sum test.