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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 citations


Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer

Nucleic Acids Res
PMCID: 5814839
PMID: 29294105
DOI: 10.1093/nar/gkx1250

[…] [SVD] 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 […]


Easy and efficient ensemble gene set testing with EGSEA

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

[…] ction Gene sets were again prioritised by their median rank across the 11 methods. > baseMethods = egsea.base()[-2] > baseMethods [1] "camera" "safe" "gage" "padog" "plage" "zscore" [7] "gsva" "ssgsea" "globaltest" "ora" "fry" > > gsam =, group=group, + probe.annot = probe.annot, + design = design, + cont […]

library_books web based topic modelling for substructure discovery in mass spectrometry

PMCID: 5860206
PMID: 28968802
DOI: 10.1093/bioinformatics/btx582

[…] isualizations. In addition, where MS1 intensity information is available for the fragmented molecules (across multiple samples), case versus control analyses can be performed. We have implemented the PLAGE method () to allow variation in MS1 intensity to be used to assess if Mass2Motifs themselves are differentially expressed. Results from such analyses can be overlaid on the network graph ().Matc […]


Detecting gene signature activation in breast cancer in an absolute, single patient manner

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 va […]


Combining multiple tools outperforms individual methods in gene set enrichment analyses

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 […]


A Pathway Based Classification Method for Analyzing Gene Expression for Alzheimer’s Disease Diagnosis

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

[…] in full time education, and APOE status (defined as the presence of any number of ɛ4 alleles) (). Two further models were built based on thesedemographic variables and gene level data (gene model) or PLAGE scores (pathway model). The purpose of the demographic model is to provide a comparator for the gene and pathway models. If models that include blood expression information (as well as demograph […]

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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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