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GSEA specifications

Information


Unique identifier OMICS_02279
Name GSEA
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

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Documentation


Maintainers


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

Additional information


http://software.broadinstitute.org/gsea/doc/desktop_tutorial.jsp

Publications for Gene Set Enrichment Analysis

GSEA in pipelines

 (191)
2018
PMCID: 5750219
PMID: 29295995
DOI: 10.1038/s41467-017-02391-6

[…] mutation. for a braf inhibitor, we show additional stratification on top of braf mutations, and for nutlin-3a on top of tp53 mutations., starting from the pathway scores derived with go/reactome gsea, spia, pathifier, paradigm, and our method on the tcga data as described above, we used cox proportional hazard model (r package survival) to calculate survival associations for pan-cancer […]

2018
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 [] (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 [], bingo [], and revigo [] […]

2018
PMCID: 5802628
PMID: 29423272
DOI: 10.1038/s41421-017-0004-z

[…] rentially expressed genes were used for pathway enrichment analysis and functional annotation of the database for annotation, visualization, and integrated discovery (david) bioinformatics resources. gsea was performed with gene signatures in gsea/msigdb v6.0, including kegg pathway signatures and go signatures. enriched gene sets or pathways were selected using a cutoff of p < 0.05 and fdr < […]

2018
PMCID: 5824024
PMID: 29385670
DOI: 10.14348/molcells.2018.2257

[…] whole degs were listed in , and arbitrarily segmented based on their transcription amplitudes (). in addition, the relative expression folds were analyzed by performing gene set enrichment analysis (gsea) (; ). to search the upstream transcription factors for the degs, enriched transcription factor binding site (tfbs) of the affected genes were queried to david functional annotation based […]

2018
PMCID: 5843367
PMID: 29300007
DOI: 10.1038/nature25140

[…] differential expression analyses were performed using the deseq2 packages,. to quantitatively compare the degree to which lps treatment induced inflammatory gene expression between species, we used gsea. gsea was performed using the desktop module available from the broad institute (https://www.broadinstitute. org/gsea/). gene ranks for contrasts of lps-treated versus untreated samples […]


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GSEA in publications

 (2048)
PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w

[…] 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 […]

PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] for the comparison of h3k4me3 changes between peak-calling algorithms, peaks called by the two algorithms assigned to the same gene were compared with each other., pathway enrichment analysis with gsea was done using the tool “run gseapreranked” in the javagsea desktop application (http://software.broadinstitute.org/gsea/downloads.jsp). gene sets h (hallmark gene sets), c1 (positional gene […]

PMCID: 5953949
PMID: 29765016
DOI: 10.1038/s41467-018-04234-4

[…] using the r/bioconductor gostats package (v.2.36.0) and considered dependencies and similarities in calculating go term p values, which were subsequently fdr corrected. gene set enrichment analysis (gsea) used the pre-ranked option based on the significance of differential expression determined by edger. k-means clustering was performed using the “kmeans” function of the “stats” package […]

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

[…] 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 […]

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

[…] status of the patients was collected from publications arising from target or pcgp that described the results of the analyses of the patient data, , . differential gene expression analysis and gsea were conducted with data on patients with explicit information of ikzf1 alteration; the number of qualified samples (196 and 107 in gse11877 and the egad00001001016 cohort, respectively) […]


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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

 (3)
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Gyan Prakash Mishra

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