ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks

Bioinformatics. 2011 Apr 15;27(8):1152-4. doi: 10.1093/bioinformatics/btr092. Epub 2011 Feb 23.

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.

Availability: ACT is available at http://act.gersteinlab.org

Contact: pi@gersteinlab.org.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genomics / methods*
  • Polymorphism, Single Nucleotide
  • Software*
  • Transcription Initiation Site