GSEA pipeline

GSEA specifications


Unique identifier OMICS_02279
Alternative names Gene Set Enrichment Analysis, GSEA-P
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, R
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 3.0
Stability Stable
Registration required Yes
Maintained Yes


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  • person_outline GSEA <>
  • person_outline Jill Mesirov <>
  • person_outline Eric Lander <>

Additional information

Publications for Gene Set Enrichment Analysis

GSEA IN pipelines

PMCID: 5801803
PMID: 29409495
DOI: 10.1186/s13045-018-0560-1

[…] was used for the datamining and bioinformatic analyses in this study. clustering and heat map visualization was performed using the mev software, version 4.9. gene set enrichment analysis [31] (gsea) was employed to demonstrate the association between our genes of interest and defined gene sets. the gene annotation network analysis was performed using the gather [32], bingo [33], and revigo […]

PMCID: 5882905
PMID: 29615825
DOI: 10.1038/s41598-018-24005-x

[…] from the ucsc genome browser ( promoters are defined as refseq transcription start site (tss) ±2 kb. biological pathways and gene sets enrichment were performed using gsea31. predicted mouse enhancer regions were obtained from a study using the mouse encode data84; enhancer prediction was based on chip-seq data of multiple tissues and cell types84. data originally […]

PMCID: 5885026
PMID: 29615509
DOI: 10.1128/mBio.02401-17

[…] ratios of ≥1.5 were counted as changed in expression., heat maps were generated using gene e ( venn diagrams were created using biovenn (41)., gsea software, available through the broad institute at, was the enrichment analysis software we used to determine whether defined sets of differentially […]

PMCID: 5928229
PMID: 29736411
DOI: 10.1038/s41523-018-0062-x

[…] old-change 1.5 and adjusted p-value cutoff <0.05 were used to identify differentially expressed genes. log10 p-values from the differential analysis were used to build the rank file for pre-ranked gsea against the cancer hallmark pathways.48,49 numbers of mice included in each analysis were as follows: p0 mfp tumors, n = 3; p0 lung metastases n = 4; p2 mfp tumors, n = 3; p2 lung metastases, n = […]

PMCID: 5928624
PMID: 29532879
DOI: 10.3892/mmr.2018.8722

[…] (26). the purpose of the hierarchical clustering analysis was to intuitively observe the differences in prognosis-associated gene expression between samples., the gene set enrichment analysis (gsea) database ( (27) is a microarray data analysis tool containing multiple functions and pathways. all the pathway annotation files of 217 biocarta pathways and 186 […]

GSEA institution(s)
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Institute for Genome Sciences and Policy, Center for Interdisciplinary Engineering, Medicine, and Applied Sciences, Duke University, Durham, NC, USA; Department of Medical Oncology, Dana–Farber Cancer Institute, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, , Boston, MA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Neurology, Children’s Hospital, Harvard Medical School, , Boston, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA

GSEA reviews

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Gyan Prakash Mishra

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Perform functional enrichment analysis on list of genes (Differentially expressed genes from cufflink or DESeq2). provides an option to choose database from MSigDB to search against.

Arup Ghosh

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The best free tool available for hassle-free gene set enrichment analysis.