Full metadata record
DC Field | Value | Language |
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dc.citation.number | 11 | - |
dc.citation.startPage | e0165919 | - |
dc.citation.title | PLOS ONE | - |
dc.citation.volume | 11 | - |
dc.contributor.author | Yoon, Sora | - |
dc.contributor.author | Kim, Seon-Young | - |
dc.contributor.author | Nam, Dougu | - |
dc.date.accessioned | 2023-12-21T23:07:50Z | - |
dc.date.available | 2023-12-21T23:07:50Z | - |
dc.date.created | 2016-11-28 | - |
dc.date.issued | 2016-11 | - |
dc.description.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 commonly 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-permuting GSEA methods for RNA-seq data. To test the performance, a simulation method to generate 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 proposed methods outperformed others that do not account for the inter-gene correlation. Analysis 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. | - |
dc.identifier.bibliographicCitation | PLOS ONE, v.11, no.11, pp.e0165919 | - |
dc.identifier.doi | 10.1371/journal.pone.0165919 | - |
dc.identifier.issn | 1932-6203 | - |
dc.identifier.scopusid | 2-s2.0-84994414322 | - |
dc.identifier.uri | https://scholarworks.unist.ac.kr/handle/201301/20771 | - |
dc.identifier.url | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165919 | - |
dc.identifier.wosid | 000387724300067 | - |
dc.language | 영어 | - |
dc.publisher | PUBLIC LIBRARY SCIENCE | - |
dc.title | Improving gene-set enrichment analysis of RNA-Seq data with small replicates | - |
dc.type | Article | - |
dc.description.isOpenAccess | TRUE | - |
dc.relation.journalWebOfScienceCategory | Multidisciplinary Sciences | - |
dc.relation.journalResearchArea | Science & Technology - Other Topics | - |
dc.description.journalRegisteredClass | scie | - |
dc.description.journalRegisteredClass | scopus | - |
dc.subject.keywordPlus | DIFFERENTIAL EXPRESSION ANALYSIS | - |
dc.subject.keywordPlus | BIOCONDUCTOR PACKAGE | - |
dc.subject.keywordPlus | NORMALIZATION | - |
dc.subject.keywordPlus | TOOLS | - |
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