ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization
Fig 4
Interpretable templates at the HCLS locus in IMR-90 cells.
a. Average chromatin contacts in cells actively transcribing (left) and non-transcribing (middle) the HCLS gene within the surrounding 10 Mb region. The right panel highlights the contrast in contact patterns, emphasizing a stronger boundary in actively transcribing cells. b. Templates generated using Non-Negative Matrix Factorization (NMF) on this cell population. Among the 20 components, five exhibit significant differences between cells transcribing and not transcribing the HCLS gene (FDR < 0.1, Benjamini-Hochberg correction). c. Directionality index of templates 0 and 11 correspond with the location of the transcribed HLCS gene. d-e. Insulation scores of templates 3 and 4 align with a shift in compartment in IMR-90 cells.