Introduction

RNA-Seq is quickly becoming the preferred method for comprehensively characterizing whole transcriptome activity, and the analysis of count data from RNA-Seq requires new computational tools. We developed GSAASeqSP, a novel toolset for genome-wide gene set association analysis of sequence count data. This toolset offers a variety of statistical procedures via combinations of multiple gene-level and gene set-level statistics, each having their own strengths under different sample and experimental conditions. These methods can be employed independently, or results generated from multiple or all methods can be integrated to determine more robust profiles of significantly altered biological pathways. Using simulations, we demonstrate the ability of these methods to identify association signals and to measure the strength of the association. We show that GSAASeqSP analyses of RNA-Seq data from diverse tissue samples provide meaningful insights into the biological mechanisms that differentiate these samples. GSAASeqSP is a powerful platform for investigating molecular underpinnings of complex traits and diseases arising from differential activity within the biological pathways. GSAASeqSP is available at http://gsaa.unc.edu.

Publications

  1. GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data.
    Cite this
    Xiong Q, Mukherjee S, Furey TS, 2014-09-01 - Scientific reports

Credits

  1. Qing Xiong
    Developer

    Department of Computer Science and Technology, Department of Statistics, China

  2. Sayan Mukherjee
    Developer

    Department of Statistical Science, Department of Computer Science, United States of America

  3. Terrence S Furey
    Investigator

    Department of Genetics, Department of Biology, United States of America

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Summary
AccessionBT006934
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByTerrence S Furey