title: GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data.
abstract: 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.
authors.affiliation: Department of Computer Science and Technology, Department of Statistics, Southwest University, Chongqing 400715, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xiong
authors.affiliation: Department of Statistical Science, Department of Computer Science, and Department of Mathematics, Duke University, Durham, NC 27708, USA.
authors.forename: Sayan
authors.initials: S
authors.lastname: Mukherjee
authors.affiliation: Department of Genetics, Department of Biology, Lineberger Comprehensive Cancer Center, and Carolina Center for Genomics and Society, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Terrence S
authors.initials: TS
authors.lastname: Furey
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics
chemical_list: D012313:RNA