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PSEA specifications


Unique identifier OMICS_13389
Alternative name Phase Set Enrichment Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data PSEA requires users to input a file that contains a list of cycling transcripts and their peak
Input format GMT
Output format SVG
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes



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  • person_outline Ron Anafi <>

Publication for Phase Set Enrichment Analysis

PSEA in publications

PMCID: 5904149
PMID: 29666379
DOI: 10.1038/s41467-018-03922-5

[…] detection, we applied the three methods and used stricter criteria: meta2d_bh.q (false discovery rate based on the integrated p values) <0.05 and meta2d_amp (the amplitude) >1. we used psea tool to cluster phase values in a given biological cluster. functional annotations were downloaded from tair database and reformatted to prepare for psea input. genes with significantly […]

PMCID: 5797448
PMID: 29404219
DOI: 10.7717/peerj.4327

[…] (). p-values of non-zero amplitude of the spline fits were calculated using 1,000 permutations of the relationship between acrophase and log2 fold-change and the method of phipson and smyth (). for phase set enrichment analysis (), we used the canonical pathways gene sets from msigdb () and looked for gene sets with a q-value ≤0.1 against a uniform distribution and vector-average value within […]

PMCID: 5692188
PMID: 29098954
DOI: 10.1177/0748730417728663

[…] encourage investigators to explore filtering their data using amplitude, fold change, and/or the signal-to-noise ratio. newer ontology analysis tools specific for biological rhythms such as phase set enrichment analysis () may also be valuable in this context when exploring enriched pathways in rhythmic data sets., the inherent imprecision of probabilistic results discussed […]

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PSEA institution(s)
Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PE, USA; Department of Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, PE, USA; Department of Medicine and Center for Sleep and Circadian Neurobiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PE, USA
PSEA funding source(s)
The authors received no financial support for this research.

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