A cistrome can be defined as a set of cis-acting elements bound by a trans-acting factor (aka transcription factor) at the genomic scale. Cistromes as such correspond to binding sites identified by ChIP-Seq experiments (Tang et al, http://cancerres.aacrjournals.org/content/71/22/6940 A major challenge is to link cistromes (or binding sites of a transcription factor) with direct target genes of that factor. However, binding sites identified by ChIP-Seq are not only found in the promoter regions of a gene but also in distal intergenic region or introns. They may contribute to regulation of gene expression through long-distance chromatin interactions. These long-distance chromatin interactions are typically studied by Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing (Lieberman-Aiden et al, http://www.sciencemag.org/content/326/5950/289 ), and ChIA-PET, a combination of the existing methods of chromatin immunoprecipitation (ChIP) and paired-end ditag (PET) sequencing (Fullwood et al, http://www.nature.com/nature/journal/v462/n7269/full/nature08497.html ). While these methods are not able to link a transcription factor binding site to its target gene, they clearly showed that interactions within single chromosomal arms exhibit in a predictable way a decrease of the contact probability P with genomic distances (Dekker et al, http://www.nature.com/nrg/journal/v14/n6/full/nrg3454.html ).
Based on the findings that (1) enhancer regulation potential is proportional to the number of binding sites near a gene and (2) that the trend of chromatin interactions diminishes in a predictable way with increasing genomic distance, Tang et al (http://cancerres.aacrjournals.org/content/71/22/6940) proposed to calculate the regulatory potential of a transcription factor for a given gene as the sum of the nearby binding sites weighted by the distance from each site to the transcription start site (TSS) of the gene.
We have adapted this method and calculated for each of the 161 transcription factors contained in the ENCODE TFBS ChIP-Seq data sets, their regulatory potential on each of the 25635 genes annotated in the human hg19 genome assembly. TFdiff ENCODE SGRA allows you (1) to identify the transcription factors having the highest regulatory potential for your gene of interest and (2) to visualize the associated ChIP-Seq peak regions for these regulatory transcription factors together with the integrated regulation from ENCODE tracks of UCSC genome (http://genome-euro.ucsc.edu/index.html) to get a useful insight in the different aspects of how your gene might be regulated.