MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites - PubMed (original) (raw)

MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites

Anthony O Olarerin-George et al. Bioinformatics. 2017.

Abstract

Summary: An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Availability and implementation: The code and associated tutorial are available at https://github.com/olarerin/metaPlotR .

Contact: srj2003@med.cornell.edu.

© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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Figures

Fig. 1.

Fig. 1.

Metagene of m6A sites. This metagene of N-6 methyladenosine sites (m6A) was generated with MetaPlotR. The metagene shows the characteristic peak in RNA methylation around the CDS end/3′UTR start. The metagene also highlights an optional feature of MetaPlotR—re-scaling of the 5′UTR, CDS and 3′UTR plotted lengths to reflect the average size of these regions in the queried dataset

References

    1. Carlile T.M. et al. (2014) Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature, 515, 143–146. - PMC - PubMed
    1. Dominissini D. et al. (2016) The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature, 530, 441–446. - PMC - PubMed
    1. Dominissini D. et al. (2012) Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature, 485, 201–206. - PubMed
    1. Kent W.J. et al. (2002) The human genome browser at UCSC. Genome Res, 12, 996–1006. - PMC - PubMed
    1. Ke S. et al. (2015) A majority of m 6 A residues are in the last exons, allowing the potential for 3′ UTR regulation. Genes Dev., 29, 2037–2053. - PMC - PubMed

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