Supplementary Figure 12: NetSig is independent of mutation frequency and identifies more low frequency cancer genes

a) A box plot of the NetSig (red) and MutSig suite (blue) P values (x-axis) versus mutation frequency distributions (y-axis). Boxes represent median first and third quartile of the frequency distribution for a given p value bin (NetSig values are permutation-based which limits us to deriving P values >=1.0e-6). In contrast to the MutSig suite, NetSig P values are not correlated with mutation frequencies. b) The proportion of all genes in the genome mutated at high, intermediate and low frequencies are shown in columns 1-3 (all genes in the genome), columns 4-6 (all significant MutSig genes using the pan-cancer data), columns 7-9 (all significant NetSig genes using the NetSig data), 10-12 (the Cancer5000 set), 13-16 (the NetSig set).