Epigenomics Analyses
The epigenomics analysis in this section was generated using the example data in Quick Start Example through SigProfilerTopography run without probability matrices.
Output Overview¶
Epigenomics Heatmaps¶
SBS Signatures Epigenomics Heatmaps¶
Heatmap displays enrichments and depletions of SBS signatures within open chromatin, CTCF transcription factor binding sites, histone modifications, and nucleosomes. Red colours correspond to enrichments of real mutations and blue colours correspond to depletions of real mutations when compared to simulated data. The intensities of the red and blue colours reflect the degree of enrichments or depletions based on the average fold change. White colour boxes with no annotation correspond to insufficient data for performing statistical comparisons. Statistically significant enrichments and depletions are annotated with * (q-value ≤ 0.05).
Epigenomics Occupancy Plots¶
In occupancy plot, solid lines and dashed lines display the average topography feature’s signal (y-axis) along a 2 kilobase window (x-axis) centered at the somatic mutation locations for real and simulated mutations, respectively. The mutation location is annotated in the middle of each plot and denoted as 0. The 2 kilobase window encompasses 1,000 base-pairs 5’ adjacent to each mutation as well as 1,000 base-pairs 3’ adjacent to each mutation.
Open Chromatin Occupancy of Exampler Signature SBS13¶
H3K4me3 Occupancy of Exampler Signature SBS13¶