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Nucleic Acids Res. 2014 Apr;42(8):e68. doi: 10.1093/nar/gku156. Epub 2014 Feb 20.

fourSig: a method for determining chromosomal interactions in 4C-Seq data.

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  • 1Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA, Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Abstract

The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-Seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-Seq experiments generate large, complicated data sets and it is imperative that signal is properly distinguished from noise. Currently, there are a limited number of methods for analyzing 4C-Seq data. Here, we present a new method, fourSig, which in addition to being precise and simple to use also includes a new feature that prioritizes detected interactions. Our results demonstrate the efficacy of fourSig with previously published and novel 4C-Seq data sets and show that our significance prioritization correlates with the ability to reproducibly detect interactions among replicates.

PMID:
24561615
PMCID:
PMC4005674
DOI:
10.1093/nar/gku156
[PubMed - indexed for MEDLINE]
Free PMC Article
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