Additional file 9.
Figure S6 - (PPT, Powerpoint file) Histogram of the PWM-to-PWM GC content differences of co-occurring motifs predicted by three approaches. Co-occurrences predicted by the FR measure are least affected by PWM-to-PWM GC content differences. The distribution of GC content differences of predicted co-occurring pairs of PWMs is shown 1) for the 1294 PWMs found to be significantly co-occurring with an over-represented motif according to FR values ("co-occurring motifs, FR"), 2) for the PWMs found to be co-occurring with an over-represented motif according to Pocc ("co-occurring motifs, Pocc"), and 3) for the PWMs found to be co-occurring with an over-represented motif according to the approach of Sudarsanam et al. ("co-occurring motifs, Sudarsanam"). For the latter two approaches the 1294 pairs with the most significant co-occurrence were used.
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Vandenbon et al. BMC Genomics 2012 13(Suppl 7):S11 doi:10.1186/1471-2164-13-S7-S11