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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




No version available



  • person_outline Ron Anafi

Publication for Phase Set Enrichment Analysis

PSEA citations


Genome wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns

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

[…] TS oscillation 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 oscillati […]


Evidence for widespread dysregulation of circadian clock progression in human cancer

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

[…] pattern, in which genes with an acrophase near πtended to show the strongest decrease in expression in tumor samples (, P ≤ 0.001 of non-zero amplitude by permutation testing for each dataset). Using Phase Set Enrichment Analysis (), we found that genes with an acrophase near π were particularly enriched for involvement in G protein-coupled receptor signaling (). Taken together, these findings sug […]


Guidelines for Genome Scale Analysis of Biological Rhythms

J Biol Rhythms
PMCID: 5692188
PMID: 29098954
DOI: 10.1177/0748730417728663

[…] therefore 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 above has impor […]


Circadian rhythms and metabolism: from the brain to the gut and back again

Ann N Y Acad Sci
PMCID: 5428740
PMID: 27589593
DOI: 10.1111/nyas.13188

[…] an day). To extend the utility of the GSEA approach for circadian analyses, Hogenesch included the Kuiper tests among other analyses, with statistically uniform power across the cycle (referred to as phase set enrichment analysis (PSEA)).Using PSEA or other strategies to identify and understand how genes and clusters of genes are regulated by circadian phase, we can begin to design translational s […]


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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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