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Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)
Small sample sizes combined with high person-to-person variability can make it difficult to detect significant gene expression changes from transcriptional profiling studies. Subtle, but coordinated, gene expression changes may be detected using gene set analysis approaches. Meta-analysis is another...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461294/ https://www.ncbi.nlm.nih.gov/pubmed/30939133 http://dx.doi.org/10.1371/journal.pcbi.1006899 |
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author | Meng, Hailong Yaari, Gur Bolen, Christopher R. Avey, Stefan Kleinstein, Steven H. |
author_facet | Meng, Hailong Yaari, Gur Bolen, Christopher R. Avey, Stefan Kleinstein, Steven H. |
author_sort | Meng, Hailong |
collection | PubMed |
description | Small sample sizes combined with high person-to-person variability can make it difficult to detect significant gene expression changes from transcriptional profiling studies. Subtle, but coordinated, gene expression changes may be detected using gene set analysis approaches. Meta-analysis is another approach to increase the power to detect biologically relevant changes by integrating information from multiple studies. Here, we present a framework that combines both approaches and allows for meta-analysis of gene sets. QuSAGE meta-analysis extends our previously published QuSAGE framework, which offers several advantages for gene set analysis, including fully accounting for gene-gene correlations and quantifying gene set activity as a full probability density function. Application of QuSAGE meta-analysis to influenza vaccination response shows it can detect significant activity that is not apparent in individual studies. |
format | Online Article Text |
id | pubmed-6461294 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-64612942019-05-03 Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) Meng, Hailong Yaari, Gur Bolen, Christopher R. Avey, Stefan Kleinstein, Steven H. PLoS Comput Biol Research Article Small sample sizes combined with high person-to-person variability can make it difficult to detect significant gene expression changes from transcriptional profiling studies. Subtle, but coordinated, gene expression changes may be detected using gene set analysis approaches. Meta-analysis is another approach to increase the power to detect biologically relevant changes by integrating information from multiple studies. Here, we present a framework that combines both approaches and allows for meta-analysis of gene sets. QuSAGE meta-analysis extends our previously published QuSAGE framework, which offers several advantages for gene set analysis, including fully accounting for gene-gene correlations and quantifying gene set activity as a full probability density function. Application of QuSAGE meta-analysis to influenza vaccination response shows it can detect significant activity that is not apparent in individual studies. Public Library of Science 2019-04-02 /pmc/articles/PMC6461294/ /pubmed/30939133 http://dx.doi.org/10.1371/journal.pcbi.1006899 Text en © 2019 Meng et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Meng, Hailong Yaari, Gur Bolen, Christopher R. Avey, Stefan Kleinstein, Steven H. Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) |
title | Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) |
title_full | Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) |
title_fullStr | Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) |
title_full_unstemmed | Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) |
title_short | Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE) |
title_sort | gene set meta-analysis with quantitative set analysis for gene expression (qusage) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461294/ https://www.ncbi.nlm.nih.gov/pubmed/30939133 http://dx.doi.org/10.1371/journal.pcbi.1006899 |
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