PMC

Contribution of the S-signature (represented by the vertical blue bars) to each lung adenocarcinoma (LUAD) sample (A) and to the head and neck squamous cell carcinoma (HNSCC) sample (B), measured by the relative coefficients. The relative coefficients were computed based on the true coefficients such that the sum of the relative coefficients for all signatures in each sample equals to 1. Blue: the S-signature. Black: the K-signature. Red: the non-CGI-signature. Yellow: the random signature.

Coefficient distribution of the L- and H-signatures in samples ordered by MLH1 gene expression level. Top panel: MLH1 gene expression relative to the house-keeping gene, TBP, sorted. Middle panel: the H-signature coefficients in each sample. Samples are listed in the same order as on the top panel. Samples with a high level of MSI are labeled in blue. Bottom panel: the L-signature coefficients in each sample. Samples are in the same order as on the top panel. The figure shows that the samples with a high coefficient of signature #1 had low expression values of MLH1 gene.

Distribution of the L- and H-signatures in colon and rectal cancer (TCGA_CRC) and endometrial carcinoma (TCGA_EC). X-axis: sample indexes. Y-axis: relative coefficient of the signature. In the L-signature, samples with a microsatellite stable status (MSS, red dots) or low levels of a microsatellite instable status (MSI-L, green dots) have high coefficients in both colon and rectal cancer (A) and endometrial carcinoma samples (B). In the H-signature, samples with high levels of MSI (MSI-H, blue dots) have high coefficient in both colon and rectal cancer (C) and endometrial carcinoma samples (D). Samples with POLE mutations were denoted by large circles.

Mutational signatures in 9 types of cancer. X-axis denotes the 96 trinucleotide substitutions. Y-axis denotes the relative coefficient of each substitution to the corresponding signature (the matrix W_96×r, see the main text). For each cancer, the plot in each panel represents one detected signature. HNSCC: head and neck squamous cell carcinoma. LUAD: lung adenocarcinoma. TCGA_BRCA: the breast cancer data from TCGA. TCGA_CRC: colon and rectal cancer. TCGA_EC: endometrial carcinoma. TCGA_GBM: glioblastoma. TCGA_OvCa: ovarian carcinoma. TCGA_SQCC: squamous cell lung cancer.