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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 citations

 (21)
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Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low‐volume, high‐intensity interval training

2017
PMCID: 5727284
PMID: 29212859
DOI: 10.14814/phy2.13534
call_split See protocol

[…] rithms through a consensus score to minimize method bias. A spectrum of GS tests was used, including both parametric (i.e., Fisher's combined probability, Stouffer's test, Reporter features test, and parametric analysis of gene set enrichment [PAGE] test) (Fisher ; Stouffer et al. ; Kim and Volsky ; Patil and Nielsen ), nonparametric methods (i.e., Tail strength test, Wilcoxon rank‐sum test, and g […]

call_split

Insight into cordycepin biosynthesis of Cordyceps militaris: Comparison between a liquid surface culture and a submerged culture through transcriptomic analysis

2017
PLoS One
PMCID: 5665525
PMID: 29091925
DOI: 10.1371/journal.pone.0187052
call_split See protocol

[…] .org/) against the Pfam database release 29.0 []. Pfam IDs were converted to Gene Ontology (GO) terms [] using the pfam2go conversion table (http://geneontology.org/external2go/pfam2go). We performed parametric analysis of gene set enrichment (PAGE) [] to define the enriched GO terms based on the logFC between the LSC and the SMC (). […]

library_books

Conserved and species specific molecular denominators in mammalian skeletal muscle aging

2017
PMCID: 5460213
PMID: 28649426
DOI: 10.1038/s41514-017-0009-8

[…] ach other on the lifespan trajectory than the middle-aged and old groups (Fig. ).Fig. 1 To further define the role of age in modifying skeletal muscle gene expression in diverse species, we performed parametric analysis of gene set enrichment (PAGE), a computational method that determines differences between genes and pathways using a priori defined gene sets. PAGE analysis revealed that as one mo […]

library_books

Determining the mode of action of anti mycobacterial C17 diyne natural products using expression profiling: evidence for fatty acid biosynthesis inhibition

2016
BMC Genomics
PMCID: 4981992
PMID: 27514659
DOI: 10.1186/s12864-016-2949-y

[…] each treatment were significantly different to the vehicle control. The GO terms that were preferentially affected by falcarinol and panaxydol treatments were determined from P-values generated from parametric analysis of gene set enrichment (PAGE) [] following a post-hoc analysis with a false discovery rate (FDR) of 0.01 (Table ). Nine common GO terms were found to be significantly different to […]

call_split

Cognitive Impairments Induced by Concussive Mild Traumatic Brain Injury in Mouse Are Ameliorated by Treatment with Phenserine via Multiple Non Cholinergic and Cholinergic Mechanisms

2016
PLoS One
PMCID: 4890804
PMID: 27254111
DOI: 10.1371/journal.pone.0156493
call_split See protocol

[…] logy 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 S […]

library_books

Generation and gene expression profiling of 48 transcription factor inducible mouse embryonic stem cell lines

2016
Sci Rep
PMCID: 4858678
PMID: 27150017
DOI: 10.1038/srep25667

[…] GNF database is quantitative and the other two are qualitative, we used different methods to quantify association: (1) correlation of median-subtracted log-transformed gene expression values, and (2) parametric analysis of gene set enrichment, PAGE (see Methods).Comparison with the GNF database showed that the induction of individual TFs shifted the transcriptome toward specific differentiation fa […]


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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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