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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Validation Study

MeSH terms

  • Alleles
  • Animals
  • Chromosomes / chemistry*
  • Data Interpretation, Statistical
  • Gene Expression
  • Genetic Loci
  • Genomics / methods
  • In Situ Hybridization, Fluorescence
  • Mice
  • Nucleic Acid Conformation
  • Software*
  • beta-Globins / genetics


  • beta-Globins

Associated data

  • GEO/GSE37275
  • GEO/GSE39406
  • GEO/GSE50907