Figure 3 : LncRNA cancer driver genes predicted by ExInAtor across cancer genomes.

From: Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features

Figure 3

(A) All driver lncRNAs (Q ≤ 0.1) and the tumour type in which they are identified. Gene names in blue indicate those belonging to CRL. (B) A mutation density plot for NEAT1 in all cancers, plotting the SNVs per kilobase as a function of gene regions. Grey represent background regions, while colours represent the mutational contribution of each cancer type to the single exon. The x-axis represents position, in bp, with respect to the start of the background region, defined here to be at 10 kb upstream of the gene’s annotated TSS. (C) The Breast mutation profile of RP11-1101K5.1, a gene with mutations in four exons. Rectangles depict mutational density of exons (blue) and introns (grey). The gene structure is indicated below, where wider portions represent exons, separated by narrower introns. (D) The Breast mutation frequency in BCAR4. (E) Percentage of genes and candidates in CNV regions and proximal to cancer-related germline SNPs. Numbers above bars indicate the absolute numbers of genes represented by each percentage. Statistical significance in each case was estimated using Fisher’s Exact test. (F) An example of an ExInAtor-predicted novel candidate gene, RP11-820L6.1. Note the presence of promoter-like histone marks (red, ChromHMM track), evolutionary conservation (PhastCons Primate conservation), and cancer SNVs around the gene TSS, as well as a proximal P53 binding site (“P53_merged”).