Fig. 9

Overlap and coverage levels of different genomic elements using enriched profiles/states in each method. Chromatin segmentation approaches are reported in columns, genomic features in rows. Each cell in the heatmap indicates the amount of overlap (a) or coverage (b) observed intersecting a feature with any profile/state specifically enriched in that feature using NMF or ChromHMM-based methods. The extent of overlap is represented as the mean percentage by which an enriched profile/state overlaps the feature (a). Similarly, we represent the coverage as the mean percentage of a given feature covered by any enriched profile/state. The color-scale (from green to purple) mirrors the amount of information retrieved for each pair of feature/method. Genomic features labels indicate: Upstream = 1kb upstream region from the Refseq TSS; CpG = CpG islands; RfTSS = genomic window of ±50bp (“Methods”) around the Refseq TSS; RfTES = genomic window of ±50bp around the Refseq TES; RfGenes(exp <25%) = Refseq genes with mean RPKM value smaller than the 25th percentile; RfGenes (exp >75%) = Refseq genes with mean RPKM value higher than the 75th percentile; PolyA = polyAdenylation-sites from PolyA-database; TFBS = conserved transcription factor binding sites; H1-enhancers = super enhancers regions precited in hESC from the dbSuper database; vistaEnhancers = experimentally validated enhancer regions in human; DNaseI = DNase hyper-sensitive sites from ENCODE project database; sRNA = predicted small RNAs