Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
Figure 2
Heatmap of ChIP-seq read density across REST peaks.
(A) Heatmap of maximal read coverage in 300 bp bins from −3.15 kb to +3.15 kb of the peak summits at all peaks identified from all 16 cell types (n = 21,134). The common peaks (top; n = 1,116), and cell-specific peaks (bottom; n = 6,003) are delineated from the remaining (middle; shared) peaks by red boxes and furthermore by blue boxes to demarcate cell-specific peaks for individual cell types. The labels for cell types are, A-A549, T-Tcell, E-ECC-1, G-GM12878, H1-H1 ESC, N-Neuron, Hc-HCT-116, Hel-HeLa S3, Hep-Hep G2, Hl-HL-60, K-K562, Pa-PANC-1, Pf-PFSK-1, S-SK-N-SH, U-U87. (B–D) Pileup of REST ChIP-seq reads mapped to three selected genes with common (B), shared (C), and cell-specific (D) peaks, as displayed in the IGV browser. In B–D, labels were used to mark cell types contained the peaks, as called by the SPP software.