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


  • Ambrosini Giovanna
  • Vorontsov Ilya
  • Penzar Dmitry
  • Groux Romain
  • Fornés Oriol
  • Nikolaeva Daria D
  • Ballester Benoit
  • Grau Jan
  • Grosse Ivo
  • Makeev Vsevolod
  • Kulakovskiy Ivan
  • Bucher Philipp


  • Transcription factor binding sites
  • PWM
  • Benchmarking
  • ChIP-seq
  • PBM

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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.

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