Fig. 4

Four classes from 109 genes. a Schematic representation of gene classification by integrating three features: (i) two-hit preference: the excess of pathogenic variants in samples with LOH compared to samples without LOH (a more positive value indicates stronger two-hit preferences), (ii) TAU score: indicating the gene expression patterns across multiple tissues (from 0 to 1, close to 1 indicates tissue-specifically expressed gene), (iii) LOEUF: the scale of predicted loss-of-function (pLoF) constraint (a higher value indicates a pLOF tolerant gene). A LEOUF score below 0.35 indicates pLOF intolerance. b Principal components analysis with three features for 109 genes. Each color represents different clusters. c Ternary plot showing the distribution of the three features across four classes. CPGs are highlighted in each plot. The size presents the excess of pathogenic variants in cases compared to control samples (Odds ratio). d Box plot presenting the distribution of assigned values for each feature across clusters. CPGs are depicted as red dots with the name of each cluster. The black dots indicate outliers, which are values between 1.5 and 3 times the interquartile ranges