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

Erik Czipa, Mátyás Schiller, Tibor Nagy, Levente Kontra, László Steiner, Júlia Koller, Orsolya Pálné-Szén, Endre Barta

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish
JournalDatabase : the journal of biological databases and curation
Volume2020
DOIs
Publication statusPublished - Jan 1 2020

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Transcription factors
Binding sites
binding sites
Transcription Factors
transcription factors
Binding Sites
Databases
Proteins
proteins
Genes
coprecipitation
protein-protein interactions
Regulator Genes
Coprecipitation
regulator genes
Single Nucleotide Polymorphism
DNA
Genome
genomics
genome

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

ChIPSummitDB : a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. / Czipa, Erik; Schiller, Mátyás; Nagy, Tibor; Kontra, Levente; Steiner, László; Koller, Júlia; Pálné-Szén, Orsolya; Barta, Endre.

In: Database : the journal of biological databases and curation, Vol. 2020, 01.01.2020.

Research output: Contribution to journalArticle

Czipa, Erik ; Schiller, Mátyás ; Nagy, Tibor ; Kontra, Levente ; Steiner, László ; Koller, Júlia ; Pálné-Szén, Orsolya ; Barta, Endre. / ChIPSummitDB : a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. In: Database : the journal of biological databases and curation. 2020 ; Vol. 2020.
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