NF-κB binds a subset of FAIRE sites independent of STAT3. (A) Transcription factor binding motifs enriched within FAIRE sites that were ±500 kb from the TSS of the genes in each indicated group. STAT3-dependent gene groups are separated based on whether their expression increases or decreases in response to siSTAT3. (B) Occupancy of NF-κB DNA binding site motifs, as a function of increasing motif quality score, within FAIRE-seq regions and in non-FAIRE regions. (C) Correlation matrix of the ChIP-seq signal at FAIRE sites. Read counts for each of the factors and conditions measured by ChIP-seq, normalized to input, were used to calculate the correlation matrix. The resulting correlation matrix is symmetric (same datasets represented on rows and columns) which was clustered by row and column to order datasets based on the similarity of binding within FAIRE sites. The correlation matrix indicates that NF-κB correlates well with itself but not to other factors, indicating that NF-κB binds an independent subset of sites. FOS and STAT3 however occupy the same FAIRE sites more frequently than other factors.