Figure 3.

MOFEXT and GeneMerge analysis of the NF-kappa B binding site. On the left side (1) we used the NF-kappa B binding site consensus (GGGRNTTTCC, where R is A or G, and N is any base). On the right side we used the exact complement of the previous site (CCCYNAAAGG, where Y is C or T). We used the same parameters for the MOFEXT search in both cases: wordsize: 7, cutoff: 70 and the subset "All promoters, subset E" (A2 and B2). After the MOFEXT search we got 10697 (NF-kappa B) and 9303 (fake site) hits. We used the score range 39-25 in both cases for the GeneMerge analysis. At the NF-kappa B site, the genes from the GO category "lymph node developments" are listed.