Single nucleotide variation (SNV) data (n = 7130) were collected across 18 cancer types from Genomic Data Commons. We estimated the mutation frequency of each circadian rhythm gene in each tumor using the maftools (https://bioconductor.org/packages/release/bioc/html/maftools.html ) and oncoplot waterfall plot [38 (link)]. We show genes with an overall mutation proportion of over 10%. SNV mutation frequency (percentage) of each gene's coding region was calculated using the formula: Number of Mutated Samples/Number of Cancer Samples. The SNVs were divided into missense mutations, nonsense mutations, multiple hits, frameshift insertions, frameshift deletions, splice sites, in-frame amplifications and in-frame deletions.
For copy number variation (CNV) data, we downloaded gene level copy number score data (GISTIC—focal score by gene) from UCSC Xena, which is the sequence interval focused on the gene and assessed whether the gene was amplified or deleted. Values between − 0.3 and 0.3 were scored as 0 for no changes, larger than 0.3 as 1 for amplifications, and less than 0.3 as − 1 for deletions. Heatmap plot of mutation frequency was generated by using ComplexHeatmap R package.
For copy number variation (CNV) data, we downloaded gene level copy number score data (GISTIC—focal score by gene) from UCSC Xena, which is the sequence interval focused on the gene and assessed whether the gene was amplified or deleted. Values between − 0.3 and 0.3 were scored as 0 for no changes, larger than 0.3 as 1 for amplifications, and less than 0.3 as − 1 for deletions. Heatmap plot of mutation frequency was generated by using ComplexHeatmap R package.
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