Optimized detection of transcription factor-binding sites in ChIP-seq experiments

Optimized detection of transcription factor-binding sites in ChIP-seq experiments

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 popu...

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Main Authors: Elo, Laura L., Kallio, Aleksi, Laajala, Teemu D., Hawkins, R. David, Korpelainen, Eija, Aittokallio, Tero
Format: Online
Language:English
Published: Oxford University Press 2012
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245948/
id pubmed-3245948
recordtype oai_dc
spelling pubmed-32459482012-01-03 Optimized detection of transcription factor-binding sites in ChIP-seq experiments Elo, Laura L. Kallio, Aleksi Laajala, Teemu D. Hawkins, R. David Korpelainen, Eija Aittokallio, Tero Methods Online 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. Oxford University Press 2012-01 2011-10-18 /pmc/articles/PMC3245948/ /pubmed/22009681 http://dx.doi.org/10.1093/nar/gkr839 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Elo, Laura L.
Kallio, Aleksi
Laajala, Teemu D.
Hawkins, R. David
Korpelainen, Eija
Aittokallio, Tero
spellingShingle Elo, Laura L.
Kallio, Aleksi
Laajala, Teemu D.
Hawkins, R. David
Korpelainen, Eija
Aittokallio, Tero
Optimized detection of transcription factor-binding sites in ChIP-seq experiments
author_facet Elo, Laura L.
Kallio, Aleksi
Laajala, Teemu D.
Hawkins, R. David
Korpelainen, Eija
Aittokallio, Tero
author_sort Elo, Laura L.
title Optimized detection of transcription factor-binding sites in ChIP-seq experiments
title_short Optimized detection of transcription factor-binding sites in ChIP-seq experiments
title_full Optimized detection of transcription factor-binding sites in ChIP-seq experiments
title_fullStr Optimized detection of transcription factor-binding sites in ChIP-seq experiments
title_full_unstemmed Optimized detection of transcription factor-binding sites in ChIP-seq experiments
title_sort optimized detection of transcription factor-binding sites in chip-seq experiments
description 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.
publisher Oxford University Press
publishDate 2012
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245948/
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