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Optimized Detection of Transcription Factor-Binding Sites in ChIP-Seq Experiments

Laura L. Elo, Aleksi Kallio, Teemu D. Laajala, R. David Hawkins, Eija Korpelainen, Tero Aittokallio, Optimized Detection of Transcription Factor-Binding Sites in ChIP-Seq Experiments. Nucleic Acids Research 40(1), e1, 2011.

Abstract:

We developed a computational procedure for optimizing the binding site detections in a given ChIP-seq experiment by maximizing their reproducibility under bootstrap sampling. We demonstrate how the procedure can improve the detection accuracies beyond those obtained with the default settings of popular peak calling software, or inform the user whether the peak detection results are compromised, circumventing the need for arbitrary re-iterative peak calling under varying parameter settings. The generic, open-source implementation is easily extendable to accommodate additional features and to promote its widespread application in future ChIP-seq studies. The peakROTS R-package and user guide are freely available at http://www.nic.funet.fi/pub/sci/molbio/peakROTS.

BibTeX entry:

@ARTICLE{jElKaLaHaKoAi11a,
  title = {Optimized Detection of Transcription Factor-Binding Sites in ChIP-Seq Experiments},
  author = {Elo, Laura L. and Kallio, Aleksi and Laajala, Teemu D. and Hawkins, R. David and Korpelainen, Eija and Aittokallio, Tero},
  journal = {Nucleic Acids Research},
  volume = {40},
  number = {1},
  pages = {e1},
  year = {2011},
}

Belongs to TUCS Research Unit(s): Biomathematics Research Unit (BIOMATH)

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