Over-representation p-values of co-occurring motifs predicted by two approaches. Co-occurrences based on Pocc are strongly biased by PWM over-representation, while this is not the case for co-occurrences predicted using the FR measure. The distribution of ORI p-values as measure for PWM over-representation is shown 1) for all PWMs in all sets of co-regulated genes ("all motifs), 2) for the 1294 PWMs found to be significantly co-occurring with an over-represented motif according to FR values ("co-occurring motifs, FR"), 3) for the PWMs found to be co-occurring with an over-represented motif according to Pocc ("co-occurring motifs, Pocc"), and 4) 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.
Vandenbon et al. BMC Genomics 2012 13(Suppl 7):S11 doi:10.1186/1471-2164-13-S7-S11