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 D 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

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; PWM; Benchmarking; ChIP-seq; HT-SELEX; PBM

Domains: Life Sciences [q-bio]; Quantitative Methods [q-bio.QM]; Genomics [q-bio.GN]

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, 2020, 21 (1), ⟨10.1186/s13059-020-01996-3⟩. ⟨hal-02773294⟩