title: ACT: aggregation and correlation toolbox for analyses of genome tracks.
abstract: We have implemented aggregation and correlation toolbox (ACT), an efficient, multifaceted toolbox for analyzing continuous signal and discrete region tracks from high-throughput genomic experiments, such as RNA-seq or ChIP-chip signal profiles from the ENCODE and modENCODE projects, or lists of single nucleotide polymorphisms from the 1000 genomes project. It is able to generate aggregate profiles of a given track around a set of specified anchor points, such as transcription start sites. It is also able to correlate related tracks and analyze them for saturation--i.e. how much of a certain feature is covered with each new succeeding experiment. The ACT site contains downloadable code in a variety of formats, interactive web servers (for use on small quantities of data), example datasets, documentation and a gallery of outputs. Here, we explain the components of the toolbox in more detail and apply them in various contexts.
  
  
  BACKGROUND
  ACT is available at http://act.gersteinlab.org
  
  
  BACKGROUND
  pi@gersteinlab.org.
authors.affiliation: Program in Computational Biology and Bioinformatics, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Jee
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.forename: Kevin Y
authors.initials: KY
authors.lastname: Yip
authors.forename: Lucas
authors.initials: L
authors.lastname: Lochovsky
authors.forename: Robert
authors.initials: R
authors.lastname: Bjornson
authors.forename: Guoneng
authors.initials: G
authors.lastname: Zhong
authors.forename: Zhengdong
authors.initials: Z
authors.lastname: Zhang
authors.forename: Yutao
authors.initials: Y
authors.lastname: Fu
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D023281:Genomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software; D024363:Transcription Initiation Site