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GSEA specifications


Unique identifier OMICS_02279
Alternative names Gene Set Enrichment Analysis, GSEA-P
Software type Application/Script
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


No version available



  • person_outline GSEA
  • person_outline Jill Mesirov
  • person_outline Eric Lander

Additional information

Publications for Gene Set Enrichment Analysis

GSEA citations


Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross linking

Nat Commun
PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w
call_split See protocol

[…] e lowest 1/8 of the dataset, or iii) for which samples having a signal (defined as a value ≥ 0.5) were strictly in the lowest 1/8 of the dataset, were disregarded. Then, Gene Set Enrichment Analysis (GSEA) was run using this trimmed matrix of gene expression (with 17,398 genes) after splitting (inside the categorical class (cls) file) the samples of the four subtypes into the two groups CB (208 sa […]


PCGF5 is required for neural differentiation of embryonic stem cells

Nat Commun
PMCID: 5954019
PMID: 29765032
DOI: 10.1038/s41467-018-03781-0

[…] e cutoff, and only genes with a mean RPKM value >1 in at least one condition were included. For functional enrichment analysis, all genes were then ranked by log2FC and used in a weighted, pre-ranked GSEA analysis against a collection of gene sets from MSigDB and user defined gene sets by using the neurectoderm and mESC-specific gene lists. Significant associations were determined for any gene set […]


Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] statistical significance calculated using a two-tailed unpaired t-test. The mean expression was also used to correlate with CD8 positivity by IHC. Gene Set enrichment analysis was performed using the GSEA java application based upon pairwise comparisons of MAPK altered versus wild-type for curated canonical gene sets. All data are deposited in the European Genome-phenome Archive ( […]


Association between angiogenesis and cytotoxic signatures in the tumor microenvironment of gastric cancer

PMCID: 5953302
PMID: 29785121
DOI: 10.2147/OTT.S162729
call_split See protocol

[…] ov/). All gastric cancers analyzed in this study were untreated primary lesions (N = 375). Additional data sets were also downloaded from TCGA in May 2017. The Hallmark gene sets were downloaded from GSEA Molecular Signatures Database v6.0 ( […]


TGF β induces miR 100 and miR 125b but blocks let 7a through LIN28B controlling PDAC progression

Nat Commun
PMCID: 5945639
PMID: 29748571
DOI: 10.1038/s41467-018-03962-x

[…] d miR-125b in PDAC, we considered the list of genes overlapping between transcripts loaded onto AGO2 and genes down-regulated following miRNA overexpression, to select for directly regulated targets. GSEA analysis of genes down-regulated by miR-125b or miR-100 overexpression (RNA-seq) showed the highest density of 7mer-m8 interacting motifs in the top 1300 down-regulated genes (Supplementary Fig.  […]


Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes

PMCID: 5943605
PMID: 29743561
DOI: 10.1038/s41419-018-0600-3

[…] […]


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GSEA institution(s)
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Systems Biology, Alpert 536, 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, Enders 260, 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.