ChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs)
interact with DNA. A substantial fraction of these regions, however, do not contain
the cognate binding site for the TF of interest. This phenomenon might be explained
by protein-protein interactions and co-precipitation of interacting gene regulatory
elements. We uniformly processed 3727 human ChIP-seq data sets and determined the
cistrome of 292 TFs, as well as the distances between the TF binding motif centers
and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data
using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets
can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most
importantly, the MotifView and PairShiftView pages show the average distance between
motif centers and overlapping ChIP-seq peak summits and distance distributions thereof,
respectively. In addition to providing a comprehensive human TF binding site collection,
the ChIPSummitDB database and web interface allows for the examination of the topological
arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/.
The database will be regularly updated and extended with the newly available human
and mouse ChIP-seq data sets.
