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

authors

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

keywords

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

document type

ART

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.

more information