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Insights gained from a comprehensive all- against-all transcription factor binding motif benchmarking study

Giovanna Ambrosini 1 Ilya Vorontsov 2 Dmitry Penzar 2 Romain Groux 1 Oriol Fornés 3 Daria Nikolaeva 4 Benoit Ballester 5 Jan Grau 6 Ivo Grosse 6 Vsevolod Makeev 2 Ivan Kulakovskiy 2 Philipp Bucher 1
1 EPFL - Ecole Polytechnique Fédérale de Lausanne
2 RAS - Russian Academy of Sciences [Moscow]
3 UBC - University of British Columbia
4 MSU - Lomonosov Moscow State University
5 TAGC - Theories and Approaches of Genomic Complexity
6 Martin-Luther-University Halle-Wittenberg
Abstract : Background: Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological applications. This calls for comprehensive benchmarking of public PWM models with large experimental reference sets.
Keywords : Transcription factor binding sites Benchmarking ChIP-seq HT-SELEX PBM PWM
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Giovanna Ambrosini, Ilya Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornés, et al.. Insights gained from a comprehensive all- against-all transcription factor binding motif benchmarking study. Genome Biology, BioMed Central, 2020, 21 (1), ⟨10.1186/s13059-020-01996-3⟩. ⟨hal-02773294⟩

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