Specifically, POU2F1 binding sites were overrepresented among loci associated with both LINE-1 and AluYb8 extent.
None of these transcription factor binding sites were overrepresented among the secondary genes.
Our analysis revealed that Wilms' tumor suppressor 1 (Wtranscriptiontion factor binding sites are overrepresented in the BDNF-correlated genes.
Χ analysis was used to determine whether those genes with predicted miRNA binding sites were overrepresented within the list of nominally significant correlations between miRNA and mRNA.
Seven transcription factor binding sites were overrepresented in the upstream regions of 24 of 25 genes from this group (see Additional file 10, Supplemental Table 5).
The results presented in Additional file 5B show that Pax5, but not the ETS family members' binding sites, are overrepresented in the five genes of interest.
In our DE genes from one hour roots, ABZ1, Alfin1, AtMYB77, BZR1, HAHB4, MYBPH3, P, TGA1a, TGA1b, TGA2, TRAB1 and WRKY11 binding sites were overrepresented (Additional file 10).
Increased placental AluYb8 methylation was positively associated with average methylation among CpG loci found in polycomb group target genes; developmentally related transcription factor binding sites were overrepresented for differentially methylated loci associated with both elements.
Interestingly, KLF binding sites are overrepresented in glucocorticoid-regulated genes and are located near GREs in several bona fide GR target genes suggesting that these factors may co-regulate a number of GR targets.
Consistent with the previously reported role of PPARγ in repression of inflammatory genes, PPARγ binding sites are overrepresented in several LPS-induced clusters (clusters 2, 3 and 5; Figure 7A) in both datasets.
General analysis of the promoters which do not contain any putative c-Myc binding site nor any putative binding site of transcription factors (TFs) being transcriptionally induced by overexpression of c-Myc resulted in the observation that some TF binding sites are overrepresented against the control promoter background.
