ChIP-chip peaks. The significance of this coverage was assessed using two separate methods, a simple hypergeometric model and the Genome Structure Correction (GSC) statistic [ 105 ]. The hypergeometric model assessed the likelihood of set A to include 'q' base pairs of overlap with set 'B', assuming n draws without replacement from the genome where n is the base-pair coverage of set A. GSC is a more complex bootstrapping method specifically designed to calculate probabilities of overlap for sets of genomics features. For both tests it was impossible to determine with any further accuracy the probabilities of overlaps for each factor with greater significance than the de minimus probability of 1 x 10 -16 . To determine what fraction of the accessible regions was covered by one or more factors (Additional file 5 ), all of the single-nucleotide locations of 1% FDR ChIP-chip peaks [ 14 , 17 ] for all factors were merged and padded on either end by 500 bp to account for imprecision in the location of each peak. Peaks in DNaseI accessibility in stage 5 embryos were ranked from largest to smallest and divided into cohorts of 1,000 peaks. If any of the merged ChIP regions fell within 75 bp of a peak in accessibility, then that DNaseI peak was said to be 'covered' by a ChIP factor. The fraction of peaks that were bound by any of the factors was calculated as the number of 'covered' peaks divided by the number of peaks per cohort.