Additional file 3: of Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation
Creators: name: Chu, Duan
name: Wei, Lai
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Figure S1. Profiling the SNPs in cancer-related genes and other genes. a Exonic SNP density in cancer-related genes and other genes. The density is calculated by the number of exonic SNPs divided by the length (Kb) of the mRNA. P-value was calculated using Wilcoxon rank sum test. b CDS SNP density in cancer-related genes and other genes. The density is calculated by the number of CDS SNPs divided by the length (Kb) of the CDS. P-value was calculated using Wilcoxon rank sum test. c Heatmaps displaying the number of exonic SNPs in each functional category. The number (n) is transferred with log2(n + 1) for the pulchritude of the graph. “onco” denotes cancer-related genes; “non-onco” denotes other genes. Figure S2. Dilemma of cancer-related genes. a Correlation between delta codon bias and nsy/syn ratio of all genes. Genes were divided into ten bins with increasing nsy/syn ratio. b Correlation between delta codon frequency and nsy/syn ratio of all genes. Genes were divided into ten bins with increasing nsy/syn ratio. c The top 20 cancer-related genes with the highest delta codon bias and relatively low nsy/syn ratio. These genes were required to have at least two synonymous and at most two nonsynonymous SNPs. d Diagram displaying the locations of nonsynonymous and synonymous SNPs on CDSs of the 20 genes mentioned above. Nonsynonymous and synonymous SNPs were labeled by red and blue asterisks, respectively. “onco” denotes cancer-related genes; “non-onco” denotes other genes. Figure S3. Detecting the constraint in cancer-related genes using highly expressed genes. a Comparison between the nonsynonymous to synonymous ratio (nsy/syn) of cancer-related genes and other genes. P-value was calculated using Wilcoxon rank sum test. b Comparison between the pooled nsy/syn ratio of cancer-related genes and other genes. P-value was calculated using Fisher’s exact test. c Conservation level (phyloP score) of nonsynonymous and synonymous SNPs in cancer-related genes and other genes. P-values were calculated using Wilcoxon rank sum tests. d Correlation between the delta codon bias after the synonymous change and the fraction of cancer-related genes. Genes were divided into ten bins with increasing delta codon bias. “onco” denotes cancer-related genes; “non-onco” denotes other genes. Figure S4. Detecting the constraint in cancer-related genes using genes with high GC content. a Comparison between the nonsynonymous to synonymous ratio (nsy/syn) of cancer-related genes and other genes. P-value was calculated using Wilcoxon rank sum test. b Comparison between the pooled nsy/syn ratio of cancer-related genes and other genes. P-value was calculated using Fisher’s exact test. c Conservation level (phyloP score) of nonsynonymous and synonymous SNPs in cancer-related genes and other genes. P-values were calculated using Wilcoxon rank sum tests. d Correlation between the delta codon bias after the synonymous change and the fraction of cancer-related genes. Genes were divided into ten bins with increasing delta codon bias. “onco” denotes cancer-related genes; “non-onco” denotes other genes. Figure S5. Detecting the constraint in cancer-related genes using genes with low GC content. a Comparison between the nonsynonymous to synonymous ratio (nsy/syn) of cancer-related genes and other genes. P-value was calculated using Wilcoxon rank sum test. b Comparison between the pooled nsy/syn ratio of cancer-related genes and other genes. P-value was calculated using Fisher’s exact test. c Conservation level (phyloP score) of nonsynonymous and synonymous SNPs in cancer-related genes and other genes. P-values were calculated using Wilcoxon rank sum tests. d Correlation between the delta codon bias after the synonymous change and the fraction of cancer-related genes. Genes were divided into ten bins with increasing delta codon bias. “onco” denotes cancer-related genes; “non-onco” denotes other genes. (PDF 700 kb)