Supplementary Figure 10: Somatic SNVs in the functional genome.
From: Accurate identification of single-nucleotide variants in whole-genome-amplified single cells
(a) Enrichment and depletion of somatic SNVs in genomic features. The asterisks indicate a significant depletion (P < 0.01, two-tailed pair-wise t test) compared to the genome average. Data on germline polymorphisms were obtained from the 1000 Genomes Project. The error bars indicate standard deviations. Sample size n=10 for the somatic SNVs, e.g. including 4 clones and 6 single-cells. (b) Mutant genes are less highly expressed than wildtype genes. Average FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) value (red dashed line) of genes affected by somatic SNVs in their exon regions was compared with the average FPKM values (black line) of 2,000 random gene sets (same number of genes as the mutant gene set). P value was calculated from the permutation (one-tailed). The RNA sequencing data were downloaded from the ENCODE project (ID: ENCFF640FPG and ENCFF704TVE). “Densities” of y-axis are kernel density estimates using “density” function in R software with default parameters.