Identification of transcription factor binding sites using ATAC-seq View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2019-12

AUTHORS

Zhijian Li, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke, Ivan G. Costa

ABSTRACT

Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints. More... »

PAGES

45

References to SciGraph publications

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-019-1642-2

    DOI

    http://dx.doi.org/10.1186/s13059-019-1642-2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1112388860

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30808370


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    N-Triples is a line-based linked data format ideal for batch operations.

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    Turtle is a human-readable linked data format.

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    RDF/XML is a standard XML format for linked data.

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