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

Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

mRNA-seq Cross-species Transcriptome Bioinformatics Gene function 

Notes

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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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Oregon State UniversityCorvallisUSA

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