Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates
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Mendeley | Further Information

{"title"=>"Improving gene-set enrichment analysis of RNA-Seq data with small replicates", "type"=>"journal", "authors"=>[{"first_name"=>"Sora", "last_name"=>"Yoon", "scopus_author_id"=>"56195029800"}, {"first_name"=>"Seon Young", "last_name"=>"Kim", "scopus_author_id"=>"48662430300"}, {"first_name"=>"Dougu", "last_name"=>"Nam", "scopus_author_id"=>"7101917725"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0165919", "sgr"=>"84994414322", "scopus"=>"2-s2.0-84994414322", "issn"=>"19326203", "pui"=>"613146297"}, "id"=>"e3989ac9-0f5b-337f-b0cf-919dc12cdcc8", "abstract"=>"Deregulated pathways identified from transcriptome data of two sample groups have played a key role in many genomic studies. Gene-set enrichment analysis (GSEA) has been com-monly used for pathway or functional analysis of microarray data, and it is also being applied to RNA-seq data. However, most RNA-seq data so far have only small replicates. This enforces to apply the gene-permuting GSEA method (or preranked GSEA) which results in a great number of false positives due to the inter-gene correlation in each gene-set. We demonstrate that incorporating the absolute gene statistic in one-tailed GSEA considerably improves the false-positive control and the overall discriminatory ability of the gene-permut-ing GSEA methods for RNA-seq data. To test the performance, a simulation method to gen-erate correlated read counts within a gene-set was newly developed, and a dozen of currently available RNA-seq enrichment analysis methods were compared, where the pro-posed methods outperformed others that do not account for the inter-gene correlation. Anal-ysis of real RNA-seq data also supported the proposed methods in terms of false positive control, ranks of true positives and biological relevance. An efficient R package (AbsFilterG-SEA) coded with C++ (Rcpp) is available from CRAN.", "link"=>"http://www.mendeley.com/research/improving-geneset-enrichment-analysis-rnaseq-data-small-replicates-1", "reader_count"=>29, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>7, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>7, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Chemistry"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}}, "reader_count_by_country"=>{"Netherlands"=>1, "Australia"=>1}, "group_count"=>1}

Scopus | Further Information

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