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Fig. 2 | BMC Medical Genomics

Fig. 2

From: The role of Neanderthal introgression in liver cancer

Fig. 2

Genes with enrichment of somatic mutations on Neanderthal haplotypes have higher expression of Neanderthal alleles. Violin plots of the proportion of reads supporting the Neanderthal allele for all heterozygous introgressed sites for each gene, for each individual in A Europeans and B East Asians. Introgressed sites were grouped whether the site was in a gene where somatic mutations were enriched on Neanderthal haplotypes for that gene (dark red) or whether the site was in a gene that did not have an enrichment of somatic mutations on either the modern or Neanderthal haplotypes for that gene (light pink). We also plotted the proportion of reads supporting the Neanderthal allele for all heterozygous introgressed sites for each gene, for each individual grouped by the genes that had an enrichment of somatic mutations on introgressed haplotypes in C Europeans and D East Asians. Each point in these plots represents the proportion of reads supporting the Neanderthal allele for an individual at a particular gene; if an individual had more than one introgressed site within a gene, the proportion of reads supporting the Neanderthal allele was averaged across these sites. The median proportion of reads supporting the Neanderthal allele for each category and gene is shown as a solid horizontal line. Dashed red horizontal line represents equal expression of both the Neanderthal and modern allele

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