Fig. 4

Illustrative example of analysis in the region of the a bait for the antisense gene AC009505.2 and an alternative promoter of NCK2 in non-activated CD4 ⁺ T cells. The top three panels show raw counts, adjusted residuals, CHiCAGO scores, and MPPC. The MPPC is overlaid on shading highlighting regions of active chromatin derived by aggregating states from CHROMHMM analysis ChIP-seq data from the same cell type, as previously published [7]. Note that the long run of fragments to the left of the promoter with high CHiCAGO scores have MPPC profiles which visually cluster into two groups, each corresponding to regions with active chromatin marks (i.e. they overlie shaded regions). The next three panels show three examples of this CHiP-seq data: H3K27ac, H3K4me1, H3K4me3. The final panel shows gene locations. The red vertical line shows the location of the bait fragment