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Fig. 2 | Genome Biology

Fig. 2

From: OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

Fig. 2

Results of the application of OncodriveFML to identify driver protein-coding genes across four cohorts of tumors. a Quantile-quantile (QQ) plots comparing the expected and observed distribution of FM bias p values of genes. Gray dots denote p values obtained on the randomized dataset that serves as negative control. Names in red indicate genes with FM bias q-value below 0.1, while names in black indicate genes with FM bias q-value below 0.25. Names in bold denote genes annotated in the Cancer Gene Census (CGC). b Mutation needle-plots showing the distribution of mutations along the sequences of the CDS of selected genes. The color of the circles follows the FI CADD score scale. The y-axis indicates the number of tumor samples in the cohorts where mutations at each position have been observed. The behavior of the CADD FI score across the entire CDS is shown below the needle-plot. c Fold increase in the proportion of CGC genes among sets with increasing number of top ranking genes detected by four methods: OncodriveFML, OncodriveFM, MutSigCV, and e-Driver. (See details in the text.) QQ plots and fold CGC proportion increase graphs for other 15 cohorts of tumors are available in Additional file 2, section A

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