Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt (original) (raw)

Nature Protocols volume 4, pages 1184–1191 (2009)Cite this article

Abstract

Genomic experiments produce multiple views of biological systems, among them are DNA sequence and copy number variation, and mRNA and protein abundance. Understanding these systems needs integrated bioinformatic analysis. Public databases such as Ensembl provide relationships and mappings between the relevant sets of probe and target molecules. However, the relationships can be biologically complex and the content of the databases is dynamic. We demonstrate how to use the computational environment R to integrate and jointly analyze experimental datasets, employing BioMart web services to provide the molecule mappings. We also discuss typical problems that are encountered in making gene-to-transcript–to-protein mappings. The approach provides a flexible, programmable and reproducible basis for state-of-the-art bioinformatic data integration.

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Acknowledgements

We thank Arek Kasprzyk and Rhoda Kinsella for insightful discussions.

This work was partially funded by the U24 CA126551 grant.

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Authors and Affiliations

  1. Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Steffen Durinck & Paul T Spellman
  2. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Ewan Birney & Wolfgang Huber

Authors

  1. Steffen Durinck
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  2. Paul T Spellman
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  3. Ewan Birney
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  4. Wolfgang Huber
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Corresponding author

Correspondence toSteffen Durinck.

Supplementary information

Supplementary Data 1

Zip archive containing the raw data of the Neve et al. study on a panel of 51 breast cell lines. It consists of Affymetrix CEL files of gene expression measurements deposited in ArrayExpress as experiment E-TABM-157, and Array CGH and protein quantification data which are available from http://cancer.lbl.gov/breastcancer. (ZIP 168067 kb)

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Durinck, S., Spellman, P., Birney, E. et al. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.Nat Protoc 4, 1184–1191 (2009). https://doi.org/10.1038/nprot.2009.97

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