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

doi:10.1101/652420

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. Protein-protein interactions, co-binding, and DNA looping can explain this phenomenon. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome for 292 TFs together with the distances between the TF binding site (TFBS) centers and the ChIP-seq peak summits. In addition to providing a comprehensive human TFBS collection, the ChIPSummitDB database and web interface allows to examine the topological arrangements of TF complexes on the DNA.

Footnotes

http://summit.med.unideb.hu/summitdb/

List of abbreviations

Bp: base pair
BWA: Burrows-Wheeler Aligner
ChIP-seq: Chromatin Immunoprecipitation Sequencing
CTCF: CCCTC-binding factor
DB: Database
dbSNP: Single Nucleotide Polymorphism Database
ELF1: E74-like factor 1
ETS1: E26 Oncogene Homolog 1
GATA1: GATA-binding factor 1
GM12878: Lymphoblastoid cell line
HOMER: Hypergeometric Optimization of Motif EnRichment
HTML: HyperText Markup Language
HTTP: HyperText Transfer Protocol
ID: identification number/identifier
NCBI: National Center for Biotechnology Information
NFYB: Nuclear transcription factor Y subunit beta
PHP: Hypertext Preprocessor
PWM: Position weight matrix
RAD21: Double-strand-break repair protein (Scc1, Mcd1)
SA1: Stromal Antigen 1
SMC1/3: Structural maintenance of chromosomes proteins
SNP: Single Nucleotide Polymorphism
SQL: Structured Query Language
SRA: Sequence Read Archive
TAL1: T-cell acute lymphocytic leukemia protein 1
TF: transcription factor
TFBS: transcription factor binding site
USF1: Upstream stimulatory factor 1
XML: Extensible Markup Language
YY1: Yin Yang 1
ZNF143: Zinc Finger Protein 143

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