Finally, we were able to identify common EN/GsbN binding sites corresponding to loci in which EN-regulated genes have been previously identified [18], [19], [21].
To demonstrate a direct interaction between miR-155 and the FOXO3a 3'-UTR, we sequentially mutated these four binding sites corresponding to the miR-155 seed regions (Figure 4B).
Structural and functional analyses of 18 mutants revealed two independent binding sites corresponding to the dual activities of HWTX-XI: strong inhibition of serine proteases and weak inhibition of Kv channels.
In other words, as N increases, the number of genes with products corresponding to a binding site of gene i increases (in-degree), and the number of genes with binding sites corresponding to the product of gene i increases (out-degree).
This fact makes it difficult to detect all the binding sites corresponding to a global regulator without a specific definition of their binding sequence on the DNA.
An interesting aspect of this bioinformatic analysis is the detection of several potential AtoC binding sites, corresponding to the pattern of motif 1, within gene-encoding regions.
Reassuringly, our high-confidence peak calls include binding sites corresponding to many known target genes, including Pck1, Ppargc1a, and Crem (Additional file 1: Figure S3).
However, there were additional H4K5Ac binding sites in the SM (87,089 H4K5Ac binding sites corresponding to 10,463 annotated genes), MS (50,031 binding sites, 9,877 genes), and the MM (74,856 binding sites, 10,301 genes) groups in comparison to the control animals that showed 22,262 H4K5Ac binding sites corresponding to 8,203 annotated genes in the rat striatum.
To identify those promoters with binding sites corresponding to binding motifs obtained from the Biobase Transfac database release 2009.3 (BIOBASE GmbH, Wolfenbuettel, Germany), we used the MotifLocator algorithm [50] with a first order background model [51].
