Table 5. NF-κB Enriched Targets.

Regulation	Pattern	Time (Hr)	Transcripts		NF-κB Sites
			ALL NF-κB	Prom	Total	Unique
Down	18/1	2	18.7	31.3	3.3	1.7
		5	17.2	27.2	2.1	1.5
Up		2	12.6	23.3	2.4	1.3
		5	18.3	30.3	2.5	1.3
Down	90/5	2	13.5	23.5	1.0	0.8
		5	10.7	18.5	0.7	0.6
Up		2	19.6	30.6	3.0	1.4
		5	25.1	36.5	4.5	2.5

NF-κB sites are enriched in transcripts following 5 hr stimulation by the 90/5 pattern. Transcripts up- and down-regulated by patterned stimulation for 2 hr and 5 hr by 18/1 or 90/5 stimulation patterns ( >1.4-fold and p < 0.05) were analyzed by DIRE. Transcripts containing NF-κB sites (NF-κB, NF-κB p50, and NF-κB p65) were filtered and summarized by transcript and TFBS. For NFK analysis by transcripts, the % of NFK-containing transcripts to total transcripts (Transcripts within proximal promoter or across intergenic, upstream, and ECRs) is given. For NF-κB TFBS analysis by site, unique sites or total # of observations were considered. In all 4 types of analysis, there was significant enrichment in NFK sites for 5 hr at 90/5 [Mean and 95% confidence interval for transcripts: 17.0 ± 3.2% (All NF-κB), 27.6 ± 3.9% (Promoter only); for NF-κB sites: 2.4 ± 0.8% (Total) and 1.4 ± 0.4% (Unique)].