RT Journal Article
SR Electronic
T1 ChIPSummitDB: A ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 652420
DO 10.1101/652420
A1 Czipa, Erik
A1 Schiller, Mátyás
A1 Nagy, Tibor
A1 Kontra, Levente
A1 Steiner, László
A1 Koller, Júlia
A1 Pálné-Szén, Orsolya
A1 Barta, Endre
YR 2019
UL http://biorxiv.org/content/early/2019/05/29/652420.abstract
AB 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.Bpbase pairBWABurrows-Wheeler AlignerChIP-seqChromatin Immunoprecipitation SequencingCTCFCCCTC-binding factorDBDatabasedbSNPSingle Nucleotide Polymorphism DatabaseELF1E74-like factor 1ETS1E26 Oncogene Homolog 1GATA1GATA-binding factor 1GM12878Lymphoblastoid cell lineHOMERHypergeometric Optimization of Motif EnRichmentHTMLHyperText Markup LanguageHTTPHyperText Transfer ProtocolIDidentification number/identifierNCBINational Center for Biotechnology InformationNFYBNuclear transcription factor Y subunit betaPHPHypertext PreprocessorPWMPosition weight matrixRAD21Double-strand-break repair protein (Scc1, Mcd1)SA1Stromal Antigen 1SMC1/3Structural maintenance of chromosomes proteinsSNPSingle Nucleotide PolymorphismSQLStructured Query LanguageSRASequence Read ArchiveTAL1T-cell acute lymphocytic leukemia protein 1TFtranscription factorTFBStranscription factor binding siteUSF1Upstream stimulatory factor 1XMLExtensible Markup LanguageYY1Yin Yang 1ZNF143Zinc Finger Protein 143