Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns
Fig 4
Visualizations of SAGA annotations.
(A) Genome browser display showing 164 cell type annotations for a 20-kbp region on human chromosome 15 (GRCh37/hg19) [76]. Each annotation has 8 labels: Promoter (red), Enhancer (orange), Transcribed (green), Permissive regulatory (yellow), Bivalent (purple), Facultative heterochromatin (light blue), Constitutive heterochromatin (black), Quiescent (gray), and Low Confidence (light gray). (B) Importance score (CAAS) for the same region. Total height at each position indicates the position’s estimated importance. Height of a given color band denotes the contribution toward importance of the associated label. (C) Genome-wide visualization of the SAGA annotation for 164 samples aggregated over GENCODE [77] protein-coding gene components. Rows: the 9 labels of the annotation. Columns: gene components, including 10 kbp flanking regions upstream and downstream. Each cell shows the enrichment of the row’s label with a position along the column’s component. Figures derived from [14]. CAAS, conservation-associated activity score; SAGA, segmentation and genome annotation.