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Unique identifier OMICS_18764
Name PAGE
Alternative name Parametric Analysis of Gene set Enrichment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.0.2
Stability Stable
Requirements
R, methods
Maintained Yes

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  • person_outline Seon-Young Kim <>
  • person_outline David Volsky <>

Publication for Parametric Analysis of Gene set Enrichment

PAGE in publications

 (24)
PMCID: 5011650
PMID: 27597445
DOI: 10.1038/srep32523

[…] accounts for differences in signature size and allows the normalized enrichment scores (ness) to be compared across all signatures. for comparison purposes we also use two other gene-set methods, parametric analysis of gene set enrichment (page) and generally applicable gene set enrichment (gage) on some of the results. computation in gsea is carried out using tools provided by the gsea […]

PMCID: 4890804
PMID: 27254111
DOI: 10.1371/journal.pone.0156493

[…] or pathways), values that are illustrated in graphical format are represented as an overall geometric average change in gene/gene set regulation between treatment groups. all data sets underwent parametric analysis of gene set enrichment analysis (page, []) for gene ontology. regulation of canonical and non-canonical pathways was assessed by use of ingenuity pathway analysis (ipa, ingenuity […]

PMCID: 4908485
PMID: 27252251
DOI: 10.14814/phy2.12785

[…] raw microarray data were normalized using a robust multiarray analysis (rma) method. to identify the pathways that were significantly altered by n‐3 pufa therapy, normalized data were subjected to parametric analysis of gene set enrichment (page) by using the r statistical software package (available at http://www.bioconductor.org) as previously described (kim and volsky ; yoshino et al. ; […]

PMCID: 4858678
PMID: 27150017
DOI: 10.1038/srep25667

[…] clustering, and then sorted manually., comparison of gene expression changes induced by tf manipulation with functionally annotated gene sets (i.e., go, gad, and sets of tf targets) was done using parametric analysis of gene set enrichment, page, implemented in exatlas. page was applied separately to upregulated genes (25% top genes sorted by logratio of dox− vs. dox+ ) and downregulated genes […]

PMCID: 4726092
PMID: 26780889
DOI: 10.1038/srep19429

[…] significant using the hyst test and also a hypergeometric test enrolling genes with a p-value of 0.001. we also performed a pathway analysis using an alternative program, gsa-snp, using the page (parametric analysis of gene set enrichment) method. when using gsa-snp, we selected the snp with the 2nd lowest p-value to define the gene p-values, and used a padding window of 10 kb. the program […]


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PAGE institution(s)
Molecular Virology Division, St. Luke's-Roosevelt Hospital Center and Columbia University, New York, NY, USA; Human Genomics Laboratory, Genome Research Center, Korea Research, Institute of Biosciences and Biotechnology Daejon, Korea; Molecular Virology Division, St. Luke's-Roosevelt Hospital Center, New York, NY, USA
PAGE funding source(s)
Supported by grants NS31492 and DA17618 from the National Institutes of Health.

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