Figure 1
From: Homologous repair deficiency score for identifying breast cancers with defective DNA damage response
Characterization of four mutational signatures. (A) Characterization of four distinct mutational signatures. Trinucleotide 96 plot for the finally selected mutational signatures. Different colours represent one of the six base substitutions, and each base substitution is categorized according to the 5′ and 3′ nucleotides. Each signature is named based on the closest Cosmic signature. W1 sig. is C > T CpG signature (cosmic 1) with cosine similarity 0.94; W2 sig. is APOBEC signature (cosmic 2 + 13) with cosine similarity 0.85 (cosmic 2) and 0.81 (cosmic 13); W3 sig. is BRCA signature (cosmic 3) with cosine similarity 0.86; W4 sig. is MSI signature (cosmic 6) with cosine similarity 0.83. (B) The relationship between subtype and mutational signatures. For each PAM50 subtype, the distribution of first signature activity is expressed as a bar graph. (C) The non-silent mutation rate based on PAM50 subtype. (D) The relationship between subtype and IFN-γ signature. IFN-γ signature was estimated by the man of the expression of six genes (IDO-1, CXCL10, CXCL9, HLA-DRA, STAT1, IFNG). (C,D) The central line in the box plot represents the median. Wilcoxon rank-sum test p-value was calculated based on one versus rest. (E) The relationship between mutation burden and signature. The scatter plot shows only the samples with signature activity ≥ 0.5, after removing the outlier based on the Tukey rules. R2 and p refer to the R-squared value and the p-value of the linear model, and the blue line represents the regression trend line. Tukey's rule is as follows: For first quartile Q1, second quartile Q2, third quartile Q3, and IQR = Q3–Q1; samples smaller than Q1–1.5IQR or larger than Q3 + 1.5IQR are regarded as outliers and removed.
