In Wee1 inhibitor contrast to c-MYC, MYCN appears to occupy sites with a higher frequency of CATGTG and CACCTG . Here, we have determined whether the frequency of E-box usage by MYCN is dependent upon its interaction with MeCP2 at regions with and without detectable levels of DNA methylation. Using supervised motif analysis of the promoter array results, we examined the frequency of all combinations of CANNTG E-box motifs across the various intersections of the MeCP2, MYCN and MeDIP datasets, along with the frequency of each motif in the background data set . For hypermethylated regions cooccupied by MeCP2 and MYCN, a higher frequency of CATGTG and CACCTG Abmole Company Z-VAD-FMK occurs, similar to our previous analysis based on MYCN binding alone . There was no significant enrichment for the MeCP2 A/T rich consensus motif, as previously described by Klose et al . Interestingly, the classic c-MYC binding motif CACGTG was highly enriched where MeCP2 was bound to hypermethylated regions in the absence of MYCN . These sites were also enriched for the CACCTG motif and the MeCP2 A/T rich consensus motif . Similar analysis of the custom tiling array revealed that such a shift in E-box preference is not observed in hypermethylated binding sites in intergenic regions . For unmethylated MYCN and MeCP2 genomic sites, there was less enrichment for E-boxes in general , with no clear preference for any particular E-box variant. This was also the case for regions only occupied by MeCP2 . To investigate other potential transcription factors that might be associated with MYCN/MeCP2 co-binding sites, we determined if other transcription factor binding motifs were significantly overrepresented. We then cross referenced these significance values with the mRNA expression for these genes to establish which transcription factors were expressed in Kelly cells. The mRNA expression for each transcription factor was plotted against the significance of its motif enrichment . Transcription factors with mRNA expression greater than the median and whose motifs were significantly enriched in all sites co-bound by MYCN and MeCP2 are represented in the upper right quadrant of Figure 6A. A similar analysis was also carried out for MYCN/MeCP2 binding at sites that were hypermethylated . By way of further external validation of this model, we examined whether any known or predicted interactions existed between these putatively co-associated transcription factors.