Cargando…

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct from those used for th...

Descripción completa

Detalles Bibliográficos
Autores principales: Wilbanks, Elizabeth G., Facciotti, Marc T.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900203/
https://www.ncbi.nlm.nih.gov/pubmed/20628599
http://dx.doi.org/10.1371/journal.pone.0011471
_version_ 1782183600509157376
author Wilbanks, Elizabeth G.
Facciotti, Marc T.
author_facet Wilbanks, Elizabeth G.
Facciotti, Marc T.
author_sort Wilbanks, Elizabeth G.
collection PubMed
description Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct from those used for the analysis of ChIP-Chip experiments. The growing popularity of ChIP-seq spurred the development of many different analytical programs (at last count, we noted 31 open source methods), each with some purported advantage. Given that the literature is dense and empirical benchmarking challenging, selecting an appropriate method for ChIP-seq analysis has become a daunting task. Herein we compare the performance of eleven different peak calling programs on common empirical, transcription factor datasets and measure their sensitivity, accuracy and usability. Our analysis provides an unbiased critical assessment of available technologies, and should assist researchers in choosing a suitable tool for handling ChIP-seq data.
format Text
id pubmed-2900203
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-29002032010-07-13 Evaluation of Algorithm Performance in ChIP-Seq Peak Detection Wilbanks, Elizabeth G. Facciotti, Marc T. PLoS One Research Article Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct from those used for the analysis of ChIP-Chip experiments. The growing popularity of ChIP-seq spurred the development of many different analytical programs (at last count, we noted 31 open source methods), each with some purported advantage. Given that the literature is dense and empirical benchmarking challenging, selecting an appropriate method for ChIP-seq analysis has become a daunting task. Herein we compare the performance of eleven different peak calling programs on common empirical, transcription factor datasets and measure their sensitivity, accuracy and usability. Our analysis provides an unbiased critical assessment of available technologies, and should assist researchers in choosing a suitable tool for handling ChIP-seq data. Public Library of Science 2010-07-08 /pmc/articles/PMC2900203/ /pubmed/20628599 http://dx.doi.org/10.1371/journal.pone.0011471 Text en Wilbanks, Facciotti. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Wilbanks, Elizabeth G.
Facciotti, Marc T.
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
title Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
title_full Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
title_fullStr Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
title_full_unstemmed Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
title_short Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
title_sort evaluation of algorithm performance in chip-seq peak detection
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900203/
https://www.ncbi.nlm.nih.gov/pubmed/20628599
http://dx.doi.org/10.1371/journal.pone.0011471
work_keys_str_mv AT wilbankselizabethg evaluationofalgorithmperformanceinchipseqpeakdetection
AT facciottimarct evaluationofalgorithmperformanceinchipseqpeakdetection