ChIPSummitDB: A ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them

Abstract

16ChIP-Seq reveals genomic regions where proteins, e.g. transcription factors (TFs) 17 interact with DNA. A substantial fraction of these regions, however, do not contain the 18 cognate binding site for the TF of interest. This phenomenon might be explained by 19 protein-protein interactions and co-precipitation of interacting gene regulatory 20 elements. We uniformly processed 3,727 human ChIP-Seq data sets and determined the 21 cistrome of 292 TFs, as well as the distances between the TF binding motif centers and 22 the ChIP-Seq peak summits. 23 24ChIPSummitDB enables the analysis of ChIP-Seq data using multiple approaches. The 25 292 cistromes and corresponding ChIP-Seq peak sets can be browsed in GenomeView. 26 2/33Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView 27 and PairShiftView pages show the average distance between motif centers and 28 overlapping ChIP-Seq peak summits and distance distributions thereof, respectively. 29 30In addition to providing a comprehensive human TF binding site collection, the 31 ChIPSummitDB database and web interface allows for the examination of the 32 topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely 33 accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly 34 updated and extended with the newly available human and mouse ChIP-Seq data sets. 35Keywords 36ChIP-seq, peak summit, TF topology, transcription factor binding site (TFBS) 371. ChIP-seq data collection from public databases 125