Fig. 4

Combining degree in transcriptional network and protein interaction network improves enrichment in driver genes. a Protein interaction network. Only the top 2000 most differentially expressed proteins from the rapamycin gene expression data are shown in order to reduce the complexity of the network. Red nodes denote rapamycin driver genes. The size of the node is proportional to its degree in the pictured network. b ROC curves showing performance of three different measures – degree in transcriptional network, degree in protein interaction network, and combined network score – in identifying driver TFs. P-values are computed using Kolmogorov-Smirnov test. AUC = area under the curve. Bar graphs show odds ratio for the overlap between driver TFs and the top 20 % of TFs ranked by each of the three measures. c ROC curves for three other growth conditions, with transcriptional networks inferred using GMIT or PANDA, as indicated