Supplementary Figure 3: Quantile-quantile plot of observed versus expected NetSig P when correcting for ‘knowledge contamination’ | Nature Methods

Supplementary Figure 3: Quantile-quantile plot of observed versus expected NetSig P when correcting for ‘knowledge contamination’

From: NetSig: network-based discovery from cancer genomes

Supplementary Figure 3

Clockwise from the upper left panel: Quantile-quantile (QQ) when using all MutSig Q values for the NetSig calculation. Upper right panel: Removing the effect of ‘Cosmic classic’ genes by setting their Q to 1 in the NetSig calculation. Lower left pane: Removing the effect of ‘Cosmic classic’ and ‘recently emerging’ cancer genes by setting their Q value to 1 in the NetSig calculation. Lower right panel: QQ plot when running NetSig on a randomized network. The random network shows no inflation, showing that the NetSig method itself does not contribute to inflation.

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