Additional file 1.

Figure S1 - (PPT, Powerpoint file) Workflow of our framework for the detection of co-occurring motifs. The analysis of genome-wide tendencies starts with a set of TFBSs, predicted in promoter sequences and a set of PWMs. For each pair of motifs, FR values are calculated, and used for further analysis of genome-wide tendencies. The analysis of co-occurrences in sets of co-regulated genes similarly starts with the prediction of TFBSs. Using these, significantly over-represented TFBSs are detected, and for each motif the tendency to co-occur with each of the over-represented motifs is analysed. The significance of the co-occurrences is evaluated using a random sampling approach, sampling sequences from the genomic set of promoters.

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Vandenbon et al. BMC Genomics 2012 13(Suppl 7):S11   doi:10.1186/1471-2164-13-S7-S11