Gene functional status prediction analysis.

A: Loss of function (LOF) analysis—Predicted genes experiencing LOF are shown based on integration of DNA and RNA data. Each column represents an individual patient tumor. The central plot lists genes (Y-axis) demonstrating partial or complete LOF in each patient. The Loss of Function score plot indicates the proportion of all patients demonstrating a predicted partial or complete LOF. The right-most plot shows the breakdown of variants supporting a complete LOF only. B: Gain of function (GOF) analysis—Predicted genes experiencing GOF are shown based on integration of DNA and RNA data. Each column represents an individual patient tumor. The central plot lists genes (Y-axis) demonstrating GOF in each patient. The variant type plot indicates the proportion of all patients demonstrating a predicted GOF. Unlike the LOF predictions, a GOF prediction does not differentiate between partial and complete gain (see S1 File). (ZIP)