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...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2019-04-01
|
Series: | PLoS Computational Biology |
Online Access: | https://doi.org/10.1371/journal.pcbi.1006899 |
id |
doaj-69bbfd50bb0c4462ae1130ade74fd442 |
---|---|
record_format |
Article |
spelling |
doaj-69bbfd50bb0c4462ae1130ade74fd4422021-06-19T05:31:24ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582019-04-01154e100689910.1371/journal.pcbi.1006899Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).Hailong MengGur YaariChristopher R BolenStefan AveySteven H KleinsteinSmall 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.https://doi.org/10.1371/journal.pcbi.1006899 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hailong Meng Gur Yaari Christopher R Bolen Stefan Avey Steven H Kleinstein |
spellingShingle |
Hailong Meng Gur Yaari Christopher R Bolen Stefan Avey Steven H Kleinstein Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE). PLoS Computational Biology |
author_facet |
Hailong Meng Gur Yaari Christopher R Bolen Stefan Avey Steven H Kleinstein |
author_sort |
Hailong Meng |
title |
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_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_sort |
gene set meta-analysis with quantitative set analysis for gene expression (qusage). |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Computational Biology |
issn |
1553-734X 1553-7358 |
publishDate |
2019-04-01 |
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. |
url |
https://doi.org/10.1371/journal.pcbi.1006899 |
work_keys_str_mv |
AT hailongmeng genesetmetaanalysiswithquantitativesetanalysisforgeneexpressionqusage AT guryaari genesetmetaanalysiswithquantitativesetanalysisforgeneexpressionqusage AT christopherrbolen genesetmetaanalysiswithquantitativesetanalysisforgeneexpressionqusage AT stefanavey genesetmetaanalysiswithquantitativesetanalysisforgeneexpressionqusage AT stevenhkleinstein genesetmetaanalysiswithquantitativesetanalysisforgeneexpressionqusage |
_version_ |
1721371246547959808 |