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. Author manuscript; available in PMC: 2016 Jul 14.
Published in final edited form as: Cell Rep. 2015 Jul 2;12(2):229–243. doi: 10.1016/j.celrep.2015.06.013

Figure 2. TSS-associated Class I Sox9 ChIP-seq peaks.

Figure 2

(A) Correlation of frequencies and peak calling scores at Class I Sox9 peaks. The X-axis represents consecutive bins of high (left) to low (right) peaks with 900 peaks per bin. The Y-axis plots the frequency of Class I Sox9 peaks within each of the binned peak sets.

(B and C) Mapping of top 2,000 ranked and bottom 2,000 ranked Sox9 peaks in relation to the nearest TSS. The X-axis represents distance from the peak center to the nearest TSS and, the Y-axis represents the frequency of Sox9 peak enrichment.

(D) Sox dimeric motif frequency in Sox9 peaks around the TSS. Sox9 peaks around TSSs (+/− 3.5 kb from TSSs) were grouped into bins of 1 kb, and the frequencies of Sox dimeric motifs per peak per kb were plotted.

(E) Signal intensity plots of ChIP-seq data for Sox9, p300, and RNA Pol II in promoter regions (+/− 2 kb from TSSs) compared to input and rabbit (rb) IgG controls in relation to expressions of their associated genes. Class I Sox9 peaks were ordered according to the expression level of the nearest associated gene (highest expression level at top). ChIP-seq signals for RNA Pol II and p300 were mapped to corresponding Sox9 peak regions.

(F) GREAT GO analysis of Class I Sox9 peaks.