ArticleScientific reports2014
GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Identification and Functional Prediction of Long Non-Coding RNAs in Dilated Cardiomyopathy by Bioinformatics Analysis.Frontiers in genetics · 2021Article
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- Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges.Entropy (Basel, Switzerland) · 2020Review
- Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles.Nucleic acids research · 2020Article
- Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation.PLoS genetics · 2020Article
- Dualism of FGF and TGF-β Signaling in Heterogeneous Cancer-Associated Fibroblast Activation with ETV1 as a Critical Determinant.Cell reports · 2019Article
- Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression.Neoplasia (New York, N.Y.) · 2019Article
- Drp1 Controls Effective T Cell Immune-Surveillance by Regulating T Cell Migration, Proliferation, and cMyc-Dependent Metabolic Reprogramming.Cell reports · 2018Article
- Notch-effector CSL promotes squamous cell carcinoma by repressing histone demethylase KDM6B.The Journal of clinical investigation · 2018Article
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- Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice.Environmental health perspectives · 2017Article
- Convergent roles of ATF3 and CSL in chromatin control of cancer-associated fibroblast activation.The Journal of experimental medicine · 2017Article
- Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data.BMC genomics · 2017Article
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Authors and funding
3 authors.
Funding
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.
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