STAT3 binding positively regulates the expression of nearby genes. (A) Each STAT3 binding site was mapped to the nearest expressed RNA-seq TSS, and divided into categories based on its distance from the TSS. Twenty sets of randomly selected background sites were generated from the input control ChIP-seq library and similarly mapped relative to the RNA-seq data for comparison. (B) Scatter plot showing the expression values of all assembled transcript fragments. Expression is shown as the log₂ of the FPKM, including up-regulated transcripts (red) and down-regulated transcripts (blue). (C) Summary of selected categories of over-represented GO terms as calculated by DAVID. Up-regulated genes (not transcripts) were used to determine GO term over-representation. The GO categories are listed on the left and ranked by their associated log₁₀ P-values. (D) Scatter plot showing the association between putative STAT3 target genes and the values of the RNA-seq assembled transcripts. Transcript expression values are marked in orange if STAT3 is bound within 20 kb of the TSS. (E) Moving average plot of STAT3 binding sites. STAT3 is more probable to be bound in the vicinity of up-regulated genes. The red/blue panel shows the change in expression of each gene ranked from up-regulated to down-regulated transcripts. The black/white panel shows the presence (black) or absence (white) of STAT3 binding within 20 kb of the TSS of the transcript. Finally, the rightmost figure shows a moving average window of the density of STAT3 binding. The black dashed line is the mean, and the dashed red line represents 1 SD from the mean. STAT3 is more probable to be bound near the TSS of a gene that is up-regulated (red) as opposed to a down-regulated gene (blue).