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Fig. 2 | Genome Medicine

Fig. 2

From: A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses

Fig. 2

ChIP-sequencing analysis of genome wide distribution of RelA, RelB, p50, and p52 binding regions. a Venn diagram showing the total number and intersections of ChIP-seq regions for p50, p52, RelA, and RelB in L1236 cells. See Additional file 4: Table S2 and Additional file 2: Figure S2A for ChIP-seq data and gene assignments. b Genome-wide NF-κB subunit occupancy profiles. Left: Regions (peak summit + -500 bp) were grouped based on their profiles of ChIP enrichment over input for all four subunits using k-means clustering (k = 8). Gray bars on top indicate the ChIPed subunit. Each row represents a region that was identified as a peak for at least one of the four subunits. The distinct clusters are indicated by numbers on the left. Right: Regions were also classified by the combination of subunits based on the peak calling results. Gray bars on top indicate which combination of subunits was called. The color-coded heatmap shows the percentage of regions in each cluster with a specific combination of subunits. c Visualization of representative ChIP-seq regions (UCSC genome browser). Top, NFKBIA gene with overlapping peaks for p50, p52, RelA, and RelB in the promoter and first intron. Bottom, intron 2 of the CDH1 gene showing selective binding of p50 and p52 to two ChIP-seq regions

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