Figure 1

Overview of the approach. The procedure takes as input gene expression data during one cellular condition, known position weight matrixes (PWMs) that correspond to candidate TFs and promoter sequences. The method determines phases of presence for each present TF, and combines their binding information with genomic sequence information to identify dynamic nucleosome positions during the condition. Dark sea green squares represent nonfunctional DNA motifs (i.e. motifs unbound by the corresponding present but nonfunctional TFs), while other squares represent functional DNA motifs (i.e. motifs bound by the corresponding present and functional TFs). Gray ellipses represent nucleosomes. Green ellipses, purple pentagons and orange trapezia represent functional TFs.