Additional file 10.

Co-localization of POU5F1 and NANOG binding sites in the mouse genome based on ChIP-PET data from [1]. (A) Proportion of ChIP-POU5F1 regions with different number of ditags that were co-localized (withn 1 Kb) with ChIP-NANOG regions (number of ditags indicates binding strength); (B) Density distribution of OCT-SOX composite binding motifs at various distances from the binding site identified with ChIP-PET [1] estimated for groups of genes with ≥ 4 POU5F1 ditags, with ≥ 4 NANOG ditags, and with ≥ 4 NANOG ditags and no POU5F1 ditags. Search for binding motifs was done using components of CisView software [17], which combines pattern-matching and position-weight matrix (PWM) approaches. PWM for OCT-SOX composite binding site was taken from [1].

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Sharov et al. BMC Genomics 2008 9:269   doi:10.1186/1471-2164-9-269