Strand Asymmetry
The strand asymmetry analysis in this section was generated using the example data in Quick Start Example through SigProfilerTopography run without probability matrices.
Output Overview¶
Strand Asymmetry Plots¶
Bar Plots¶
Replication Strand Asymmetry of SBS13¶
Replicational strand asymmetry for substitution signature SBS13. In replication strand asymmetry figure, x-axis displays six substitution subtypes based on the mutated pyrimidine base: C>A, C>G, C>T, T>A, T>C, and T>G. Mutations were oriented by the pyrimidine base of the reference Watson-Crick base-pair and classified as ones occurring on the leading or lagging strand. The y-axis represents the number of mutations on leading and lagging strands. Real and simulated mutations are shown in bar plots and shaded bar plots, respectively. Statistically significant replication strand asymmetries are depicted with * (q-value ≤ 0.05).
Transcription Strand Asymmetry of SBS13¶
Exemplar transcriptional strand asymmetry analysis for substitution signature SBS13. X-axis displays six substitution subtypes based on the mutated pyrimidine base: C>A, C>G, C>T, T>A, T>C, and T>G, and the y-axis represents the number of mutations both for real and simulated mutations on transcribed and un-transcribed strands in bar plots. Simulated mutations are shown in shaded bar plots.
Genic versus Intergenic Regions of SBS13¶
Exemplar genic versus intergenic regions analyses for substitution signature SBS13. X-axis is presented in a format similar to the one in replication and transcription strand asymmetries. The y-axis represents the number of mutations on genic and intergenic regions as bar plots. Simulated mutations are shown in shaded bar plots.
Circle Bar Plots¶
Strand Asymmetry of Exampler Signature SBS13¶
Circle Plots¶
Replication Strand Asymmetry of SBS Signatures¶
Replication strand asymmetries of signatures of single-base substitutions (SBSs). Rows represent the signatures, columns display the six substitution subtypes based on the mutated pyrimidine base: C>A, C>G, C>T, T>A, T>C, and T>G together with odd ratios : 1.10, 1.20. 1.50, 1.75, and >= 2.00. SBS signatures with replication strand asymmetries on the lagging strand or on the leading strands with adjusted p values %0.05 (Fisher’s exact test corrected for multiple testing using Benjamini-Hochberg) are shown in circles with red and yellow colors, respectively. The odds ratio is defined between the ratio of real mutations and the ratio of simulated mutations, where each ratio is calculated using the number of mutations on the lagging strand and the number of mutations on the leading strand. Only odds ratios above 1.10 are shown. Circle exhibits a signature with specific replication strand asymmetry.
Transcription Strand Asymmetry of SBS Signatures¶
Transcription strand asymmetries of signatures of single-base substitutions (SBSs). Rows represent the signatures, columns display the six substitution subtypes based on the mutated pyrimidine base: C>A, C>G, C>T, T>A, T>C, and T>G together with odd ratios : 1.10, 1.20. 1.50, 1.75, and >= 2.00. SBS signatures with transcription strand asymmetries on the transcribed and/or the untranscribed strands with adjusted p values %0.05 (Fisher’s exact test corrected for multiple testing using Benjamini-Hochberg) are shown in circles with blue and green colors, respectively. The odds ratio is defined between the ratio of real mutations and the ratio of simulated mutations, where each ratio is calculated using the number of mutations on the transcribed strand and the number of mutations on the untranscribed strand. Only odds ratios above 1.10 are shown. Circle exhibits a signature with specific transcription strand asymmetry.
Genic versus Intergenic Regions of SBS Signatures¶
Somatic mutations in genic and intergenic regions for signatures of single-base substitutions (SBSs). Rows represent the signatures, columns display the six substitution subtypes based on the mutated pyrimidine base: C>A, C>G, C>T, T>A, T>C, and T>G together with odd ratios: 1.10, 1.20. 1.50, 1.75, and >= 2.00. SBS signatures with genic and intergenic regions asymmetries with adjusted p-values ≤ 0.05 (Fisher’s exact test corrected for multiple testing using Benjamini-Hochberg) are shown in circles with cyan and grey colours, respectively. The odds ratio is defined between the ratio of real mutations and the ratio of simulated mutations, where each ratio is calculated using the number of mutations in the genic regions and the number of mutations in the intergenic regions. Only odds ratios above 1.10 are shown. Circle exhibits a signature with specific genic versus intergenic regions asymmetry.
Scatter Plots¶
All Mutation Types¶
Scatter plot showing the distribution of the replication and transcription strand ratios in log10 scale of the six pyrimidine mutation classes.
All SBS Signatures¶
Scatter plot showing the distribution of replication and transcription strand ratios in log10 scale for the four mutational signatures.