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Fig. 5 | BMC Bioinformatics

Fig. 5

From: A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data

Fig. 5

Parameter estimation results. a Neutral vs. conserved regions. The height of the bars give the fold change in mutation rate in conserved regions (phyloP score =1.3838, mean of the highest quintile, see Fig. 2c compared to neutral regions (phyloP score = 0). b Early vs. late replicating regions. The height of the bars give the fold increase/decrease in mutation rate in late replicating regions (replication timing = 1) compared to early replicating regions (replication timing = 0). c Intergenic vs. gene body. The height of the bars give the fold increase/decrease in mutation rate in gene bodies compared to intergenic regions. d Low vs. high expression. The height of the bars give the fold increase/decrease in mutation rate in highly expression regions (expression value =15, approx. the mean of the highest quintile, see Fig. 2c compared to lowly expressed regions (expression value = 0). Here, only gene bodies are considered. e Mutation type are considered as the combination of substitutions and neighboring sites. The horizontal line indicates the average mutation rate for each cancer type. The height of the bars give the fold increase/decrease in mutation rate for a specific mutation type. Panel 1: Different substitution types. Panel 2: C >T mutations in different contexts. Panel 3: C >G mutations in all contexts and in TpCp[AT] contexts

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