Detecting differential binding of transcription factors with ChIP-seq

Increasing number of ChIP-seq experiments are investigating transcription factor binding under multiple experimental conditions, for example, various treatment conditions, several distinct time points and different treatment dosage levels. Hence, identifying differential binding sites across multipl...

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Veröffentlicht in:Bioinformatics 2012-01, Vol.28 (1), p.121-122
Hauptverfasser: Liang, Kun, Kele, Sündüz
Format: Artikel
Sprache:eng
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Zusammenfassung:Increasing number of ChIP-seq experiments are investigating transcription factor binding under multiple experimental conditions, for example, various treatment conditions, several distinct time points and different treatment dosage levels. Hence, identifying differential binding sites across multiple conditions is of practical importance in biological and medical research. To this end, we have developed a powerful and flexible program, called DBChIP, to detect differentially bound sharp binding sites across multiple conditions, with or without matching control samples. By assigning uncertainty measure to the putative differential binding sites, DBChIP facilitates downstream analysis. DBChIP is implemented in R programming language and can work with a wide range of sequencing file formats. Availability: R package DBChIP is available at http://pages.cs.wisc.edu/~kliang/DBChIP/ Contact: kliang@stat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btr605