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

doi:10.1093/bioinformatics/btr092

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 journal › Article › peer-review

27 Scopus citations

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 language	English (US)
Article number	btr092
Pages (from-to)	1152-1154
Number of pages	3
Journal	Bioinformatics
Volume	27
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btr092
State	Published - Apr 2011
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr092

Cite this

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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.",

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AU - Lochovsky, Lucas

AU - Bjornson, Robert

AU - Zhong, Guoneng

AU - Zhang, Zhengdong

AU - Fu, Yutao

AU - Wang, Jie

AU - Weng, Zhiping

AU - Gerstein, Mark

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ACT: Aggregation and correlation toolbox for analyses of genome tracks

Abstract

ASJC Scopus subject areas

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