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A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data

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Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1702))

Abstract

In this methods article, I describe a computational workflow for cross-species visualization and comparison of mRNA-seq transcriptome profiling data. The workflow is based on gene set variation analysis (GSVA) and is illustrated using commands in the R programming language. I provide a complete step-by-step procedure for the workflow using mRNA-seq data sets from dog and human bladder cancer as an example.

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Acknowledgments

This work was supported by the National Science Foundation (award 1553728-DBI), the PhRMA Foundation (Research Starter Grant in Informatics), the Medical Research Foundation of Oregon (New Investigator Grant), and the Animal Cancer Foundation (Comparative Oncology Award). S.A.R. thanks Shay Bracha and Cheri Goodall for kindly providing the dog bladder RNA samples that were used in the transcriptome profiling study [3], Tanjin Xu for assistance with the mRNA-seq data processing, Brent Kronmiller for help with designing the dog mRNA-seq study, and Ilya Shmulevich, Sheila Reynolds, and Matti Nykter for advice.

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Authors and Affiliations

  1. Oregon State University, 106 Dryden Hall, Corvallis, OR, 97331, USA

    Stephen A. Ramsey

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  1. Stephen A. Ramsey
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Correspondence to Stephen A. Ramsey .

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Editors and Affiliations

  1. Department of Experimental Medicine, Systems Biology Group Lab, Sapienza University of Rome, Rome, Italy

    Mariano Bizzarri

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Ramsey, S.A. (2018). A Method for Cross-Species Visualization and Analysis of RNA-Sequence Data. In: Bizzarri, M. (eds) Systems Biology. Methods in Molecular Biology, vol 1702. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7456-6_14

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  • DOI: https://doi.org/10.1007/978-1-4939-7456-6_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7455-9

  • Online ISBN: 978-1-4939-7456-6

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