Fig. 3
(Upper Panel) Network plots of the detected modules for three choices of the FDR (10−25,10−24, and 10−18). The colour of the nodes shows their p-value from low (white) to high (purple). We indicate proteins that would not have been discovered from the gene-expression data alone as squares and give their names in bold red font. (Lower Panel) The size of detected modules (blue disks) depends on the FDR. A large fraction of proteins in these modules have significant p-values (red squares), however, for all FDR >10−26, we also identify additional proteins as for a given FDR, the blue disks are to the right of the red disks