Transcription Factor Binding Site Identification

BED4‐formatted peak‐call data of each SRX for TRs (MACS2 Q‐value < 1 × 10⁻⁵) were used for this function. The location of TSSs and gene symbols were based on refFlat files (http://hgdownload.cse.ucsc.edu/downloads.html), with only protein‐coding genes being applied to this analysis. The BEDTools (ver. 2.17.0) “window” command was used to search for target genes among peak‐call data and the TSS library with a window size option (“‐w”) followed by “1000”, “5000”, or “10000”. Peak‐call data for the same antigens were collected, and MACS2 scores were indicated as heat‐map colors on the Web browser. If a gene intersected with multiple peaks of a single SRX, the highest MACS2 score was chosen for the color indication. The “Average” column at the far left of the results table shows the mean of the MACS2 scores in each row.