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PLAGE specifications


Unique identifier OMICS_26180
Alternative name Pathway Level Analysis of Gene Expression
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No


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Publication for Pathway Level Analysis of Gene Expression

PLAGE in publications

PMCID: 5814839
PMID: 29294105
DOI: 10.1093/nar/gkx1250

[…] and principal components analysis [pca]) to pre-defined gene sets, effectively yielding a single value that encapsulates the coarse coexpression behavior of all the genes in the pathway. in the pathway level analysis of gene expression (plage) method (), svd was used to obtain a ‘pathway activity level’ quantification based on the expression of genes in the pathway. a similar approach using […]

PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] gse methods to rank biologically relevant gene sets. the current version of the egsea package utilizes the analysis results of up to twelve prominent gse algorithms that include: ora , globaltest , plage , safe , zscore , gage , ssgsea , padog , gsva , camera , roast and fry . the ora, gage, camera and gsva methods depend on a competitive null hypothesis which assumes the genes in a set […]

PMCID: 5361722
PMID: 28327201
DOI: 10.1186/s13058-017-0824-7

[…] there are many pathway analysis approaches that seek to determine whether a specific molecular process or cellular response is activated, repressed, or latent in a given patient sample including pathway level analysis of gene expression (plage) [], zscore [], single sample gene set enrichment analysis (ssgsea) [], functional analysis of individual microarray expression (faime) [], gene set […]

PMCID: 5408797
PMID: 27694195
DOI: 10.1093/bioinformatics/btw623

[…] models to estimate the significance of a gene set in an experimental comparison. in other words, the gene expression data is transformed from the gene space into the gene set space. for example, the plage algorithm uses singular value decomposition (svd) of the expression matrix for a set of genes to calculate pathway scores (). similarly, gsva calculates a kolmogorov–smirnov-like rank statistic […]

PMCID: 4927941
PMID: 26484910
DOI: 10.3233/JAD-150440

[…] ad have retrospectively identified pathways altered in disease [], this is the first study to use pathway scores for each individual to build predictive models across the population. this study used pathway level analysis of gene expression (plage) to estimate pathway variability across samples in the population by calculating sample-wise pathway scores []. plage outperformed other single sample […]

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PLAGE institution(s)
Department of Biostatistics and Bioinformatics and Center for Bioinformatics and Computational Biology, Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
PLAGE funding source(s)
Supported by the NIH through the Duke University Center for Translational Research (5 P30 AI051445-03) and of the NSF through a grant to David Bird (NCSU; DBI 0077503) as well as the Duke Center for Bioinformatics and Computational Biology.

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