Overview of the method. (a) Finding over-represented single motifs from ChIP data. Target promoters of each TF are determined from ChIP data, and these promoters are searched for over-represented motifs. (b) Finding over-represented motif combinations specific to each cell-cycle phase. For all over-represented motifs found in (a), all possible first (single)-, second (double)- and third (triple)-order combinations of motifs are searched against the promoters of the G1, S, S/G2, G2/M, M/G1 or 'All' groups of cell-cycle genes. (c) When an over-represented motif combination is found, we require that the genes possessing that combination have more coherent patterns of gene expression than the patterns for the phase-specific gene group.(d) From ChIP data, we find the set of TFs (over-represented TFs, see Materials and methods) binding to the promoters with a motif combination (from (b) and (c)), and the set of TFs that can bind over-represented motifs (from (a)) constituting a motif combination. For each motif combination and its component motifs, we take the intersection of TFs from these two sets. Such intersection TFs (in bold in the (d)) are assigned to the component motifs of a combination (see Materials and methods).