Table 1.

Odds of gene regulation based on distance and location of NF-κB/RelA ChIP-Seq peaks with respect to the gene TSS

Distance Bins	Structural Location	Average odds of regulation	SD ±
0 to 2 k	upstream	6.73	0.49
−2 k to 0	intron	4.37	0.21
−2 k to 0	exon	2.19	0.03
−2 k to 0	downstream and outside transcript	2.11	0.52
−25 k to −2 k	downstream and outside transcript	2.01	0.06
2 k to 25 k	upstream	1.73	0.18
−25 k to −2 k	intron	1.39	0.04
−1 Mb to −25 k	downstream and outside transcript	1.21	0
25 k to 1 Mb	upstream	1.07	0
−1 Mb to −25 k	intron	0.85	0.05
−25 k to −2 k	exon	0.84	0.11
−1 Mb and beyond	downstream and outside transcript	0.34	0.01
1 Mb and beyond	upstream	0.32	0.07
−1 Mb and beyond	intron	0.18	0.25
−1 Mb to −25 k	exon	N/A	N/A
−1 Mb and beyond	exon	N/A	N/A

The odds of regulation are computed as ratio of frequencies of observing a given location in NF-κB/RelA ChIP-Seq peaks divided by frequencies of observing such location if peaks were randomly placed in the genome, separately for the positive and negative strands. Then, average and standard deviation was computed using data from both strands. Note that as our data includes both false positives and false negatives, the reported ratios are likely conservative estimates showing minimum possible values. ‘N/A’ indicates the cases where there was not enough data to allow estimating odds of regulation.