CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments

Dimont, Emmanuel, Hofmann, Oliver, Ho Sui, Shannan J., Forrest, Alistair R. R., Kawaji, Hideya, Hide, Winston and the FANTOM Consortium (2014) CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. Bioinformatics, 30 8: 1183-1184. doi:10.1093/bioinformatics/btu125

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Author Dimont, Emmanuel
Hofmann, Oliver
Ho Sui, Shannan J.
Forrest, Alistair R. R.
Kawaji, Hideya
Hide, Winston
the FANTOM Consortium
Title CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4811
1367-4803
Publication date 2014-04-01
Year available 2014
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btu125
Open Access Status Not Open Access
Volume 30
Issue 8
Start page 1183
End page 1184
Total pages 2
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Abstract Alternate promoter usage is an important molecular mechanism for generating RNA and protein diversity. Cap Analysis Gene Expression (CAGE) is a powerful approach for revealing the multiplicity of transcription start site (TSS) events across experiments and conditions. An understanding of the dynamics of TSS choice across these conditions requires both sensitive quantification and comparative visualization. We have developed CAGExploreR, an R package to detect and visualize changes in the use of specific TSS in wider promoter regions in the context of changes in overall gene expression when comparing different CAGE samples. These changes provide insight into the modification of transcript isoform generation and regulatory network alterations associated with cell types and conditions. CAGExploreR is based on the FANTOM5 and MPromDb promoter set definitions but can also work with user-supplied regions. The package compares multiple CAGE libraries simultaneously. Supplementary Materials describe methods in detail, and a vignette demonstrates a workflow with a real data example.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
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Created: Fri, 27 Jun 2014, 00:17:00 EST by Cathy Fouhy on behalf of Aust Institute for Bioengineering & Nanotechnology