Figure 2

Examples of TFs for which the in vitro and in vivo DNA binding site motifs are different. For both the in vitro and in vivo motifs of the three TFs we show their enrichment in the corresponding ChIP-chip data set, measured by the AUC and the associated P-value. We also show the in vitro motifs (from our curated collection) that are most similar to the in vitro and in vivo motifs of the three TFs of interest (the red lines indicate which parts of the motifs are similar). We notice that in all three cases the in vivo motifs are similar to the DNA binding site motifs of TFs from a different structural class. This suggests that in each of the three cases the in vivo motif (derived from ChIP-chip data) does not belong to the TF profiled by ChIP, but either to a co-regulatory TF (which binds a common set of targets as the profiled factor), or to a mediating TF (which binds DNA directly and mediates the interaction between the TF profiled by ChIP and the DNA - in this case we hypothesize that the TF tested by ChIP binds DNA indirectly thought the mediating TF). Motif sources from this study and Zhu et al. [11], Badis et al. [10], and MacIsaac et al. [20].