QuSAGE protocols

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QuSAGE specifications

Information


Unique identifier OMICS_09761
Name QuSAGE
Alternative name Quantitative Set Analysis for Gene Expression
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.14.0
Stability Stable
Requirements
methods, Biobase, utils, R(>=2.10), nlme, limma(>=3.14), lsmeans
Maintained Yes

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Maintainer


  • person_outline Christopher R. Bolen <>

Publication for Quantitative Set Analysis for Gene Expression

QuSAGE in pipeline

2015
PMCID: 4678663
PMID: 26667497
DOI: 10.1186/s40168-015-0133-2

[…] after filtering, the lmfit and ebayes functions were used to perform moderated paired t testing for each gene across visits 1 and 2., at this level, gene set enrichment of isg was performed with the qusage package in r [], comparing our processed gene lists against those from a prior study of a549 cell lines subjected to α or γ interferon []., genes of interest from either group […]


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QuSAGE in publications

 (7)
PMCID: 5585977
PMID: 28874170
DOI: 10.1186/s13059-017-1301-4

[…] polymerase chain reaction (qpcr), with go pathways relating to ifn response and viral defence the only pathways enriched in the differentially expressed genes (fig. ; additional file : dataset s2). quantitative set analysis for gene expression (qusage) was performed to examine the transcriptional signature of adar1-editing deficiency, defined in our previous analysis of the adar1 e861a/e861a […]

PMCID: 5148902
PMID: 27938331
DOI: 10.1186/s12859-016-1403-0

[…] we evaluated mgszm together with several gene set analysis methods from the literature: gage (generally applicable gene-set enrichment) [], camera (correlation adjusted mean rank gene set test) [], qusage (quantitative set analysis of gene expression) []) and allez [] (table 1). gage is based on parametric gene randomization and thus neglects gene-gene correlation. another major difference […]

PMCID: 4933655
PMID: 27135421
DOI: 10.1111/acel.12488

[…] between expressed genes in the aged vs. young ldlr −/− mice maintained on a chow diet compared to the other groups (fig. s7). thus, we focused on this group for our gene set analysis using qusage gene set enrichment analysis., we observed that gene sets that were upregulated within the aorta with aging included viral invasion and host response, platelet adhesion; and extracellular […]

PMCID: 4769743
PMID: 26981147
DOI: 10.1155/2016/7686081

[…] san diego, ca). illumina arrays were log-transformed and quantile-normalized by using lumi package []. the normalized expression levels were used to find activity of tfs and signaling pathways using qusage [, ]. the target genes of tfs and the genes involved in the pathways were obtained from msigdb []. particularly, gene-sets for ligand induced signaling pathways were obtained from biocarta, […]


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