ACT

Aggregation and correlation toolbox for analyses of genome tracks

Justin Jee, Joel Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert Bjornson, Guoneng Zhong, Zhengdong Zhang, Yutao Fu, Jie Wang, Zhiping Weng, Mark Gerstein

Research output: Contribution to journalArticle

25 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberbtr092
Pages (from-to)1152-1154
Number of pages3
JournalBioinformatics
Volume27
Issue number8
DOIs
StatePublished - Apr 2011
Externally publishedYes

Fingerprint

Transcription Initiation Site
Documentation
Single Nucleotide Polymorphism
Aggregation
Genome
Agglomeration
Genes
RNA
Chip
Transcription
Nucleotides
Anchors
Polymorphism
Servers
Single nucleotide Polymorphism
Experiments
Throughput
Web Server
Correlate
High Throughput

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Jee, J., Rozowsky, J., Yip, K. Y., Lochovsky, L., Bjornson, R., Zhong, G., ... Gerstein, M. (2011). ACT: Aggregation and correlation toolbox for analyses of genome tracks. Bioinformatics, 27(8), 1152-1154. [btr092]. https://doi.org/10.1093/bioinformatics/btr092

ACT : Aggregation and correlation toolbox for analyses of genome tracks. / Jee, Justin; Rozowsky, Joel; Yip, Kevin Y.; Lochovsky, Lucas; Bjornson, Robert; Zhong, Guoneng; Zhang, Zhengdong; Fu, Yutao; Wang, Jie; Weng, Zhiping; Gerstein, Mark.

In: Bioinformatics, Vol. 27, No. 8, btr092, 04.2011, p. 1152-1154.

Research output: Contribution to journalArticle

Jee, J, Rozowsky, J, Yip, KY, Lochovsky, L, Bjornson, R, Zhong, G, Zhang, Z, Fu, Y, Wang, J, Weng, Z & Gerstein, M 2011, 'ACT: Aggregation and correlation toolbox for analyses of genome tracks', Bioinformatics, vol. 27, no. 8, btr092, pp. 1152-1154. https://doi.org/10.1093/bioinformatics/btr092
Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G et al. ACT: Aggregation and correlation toolbox for analyses of genome tracks. Bioinformatics. 2011 Apr;27(8):1152-1154. btr092. https://doi.org/10.1093/bioinformatics/btr092
Jee, Justin ; Rozowsky, Joel ; Yip, Kevin Y. ; Lochovsky, Lucas ; Bjornson, Robert ; Zhong, Guoneng ; Zhang, Zhengdong ; Fu, Yutao ; Wang, Jie ; Weng, Zhiping ; Gerstein, Mark. / ACT : Aggregation and correlation toolbox for analyses of genome tracks. In: Bioinformatics. 2011 ; Vol. 27, No. 8. pp. 1152-1154.
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