Figure 3

ChIP-seq analysis of HOXC9 genomic distribution. (A) Summary of HOXC9-binding peaks and genes identified by ChIP-seq. (B-C) Scatter plot analysis (B) and ChIP-seq tag profiles of chromosome 21 (C) showing a high correlation between two independent HOXC9 ChIP-seq samples. (D) Pie chart showing genomic distribution of HOXC9-binding peaks relative to RefSeq functional categories including promoters (within 5 kb upstream of TSS), 5’ UTRs, exons, introns, 3’ UTRs, downstream (within 5 kb downstream of the gene), and intergenic regions (outside −5 ~ +5 kb of genes). (E) Bar graph showing the distribution of HOXC9-binding peaks relative to the functional categories after normalization to the size of each category in 100 kb. (F) Histogram showing the distribution of HOXC9-binding peaks relative to the nearest TSS. Peaks were combined in 100 bp. (G) Web logo showing the top enriched motif present in HOXC9 ChIP-seq peaks, which corresponds to the binding site for Abd-B, the Drosophila ortholog of mammalian HOX9-13 paralogs.