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GAGE specifications


Unique identifier OMICS_18498
Alternative name Generally Applicable Gene-set Enrichment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A gene set.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.30.0
Stability Stable
AnnotationDbi, limma, Rsamtools, GenomicAlignments, edgeR, DESeq2, DESeq, R(>=2.10), GO.db,, graph, TxDb.Hsapiens.UCSC.hg19.knownGene, GSEABase, KEGGREST, hgu133a.db, pathview, gageData
Maintained Yes




No version available



  • person_outline Peter Woolf
  • person_outline Weijun Luo
  • person_outline Michael Friedman
  • person_outline Kerby Shedden
  • person_outline Kurt Hankenson

Additional information

Publication for Generally Applicable Gene-set Enrichment

GAGE citations


Genomic alterations of ground glass nodular lung adenocarcinoma

Sci Rep
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] M-values normalization method. The differentially expressed genes were identified using the DESeq R package ( Gene set enrichment tests were performed using the GAGE R tool. Clustering was performed by principal component analysis and hierarchical clustering. Gene ontology analyses were performed by DAVID ( and visualized by REVIGO […]


Placental miR 340 mediates vulnerability to activity based anorexia in mice

Nat Commun
PMCID: 5913294
PMID: 29686286
DOI: 10.1038/s41467-018-03836-2
call_split See protocol

[…] e analysis of differentially expressed genes in gene aggregation mode, requiring q-values of <0.05 for both Wald and likelihood ratio tests, with a beta value cut-off 0.25. For KEGG pathway analysis, GAGE 2.24.0 was used with log2 transformed, filtered and normalized TPM values extracted from sleuth. An FDR of 0.1 was applied as cut-off for significance. […]


Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae

Front Microbiol
PMCID: 5917014
PMID: 29725322
DOI: 10.3389/fmicb.2018.00752
call_split See protocol

[…] ses. We report all the GO terms recovered by this approach in Supplementary Dataset . The up- or down-regulation of KEGG pathway-related gene expression was determined using z-test as implemented in “GAGE” R package (). This analysis employed input from all the genes, irrespective of fold-change level or statistical significance, and looked for coordinated expression changes within a particular pa […]


Altered function and maturation of primary cortical neurons from a 22q11.2 deletion mouse model of schizophrenia

PMCID: 5904157
PMID: 29666363
DOI: 10.1038/s41398-018-0132-8

[…] nections between transcriptome and electrophysiological features, we looked for common functional pathways among altered genes using the generally applicable gene-set enrichment for pathway analysis (GAGE), which maps the gene expression pattern onto the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). GAGE indicated an enrichment of synapse related pathways among the upregulated e […]


Low level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice

Sci Rep
PMCID: 5897405
PMID: 29651131
DOI: 10.1038/s41598-018-24290-6

[…] package. GO term and pathway enrichment analyses were performed based on the effect size between the different mouse strains or age using the generally applicable Gen Set Enrichment Analysis (GSEA), GAGE, which determines whether a set of genes is systematically up- or down-regulated as a whole. For gene set definitions, we used the Molecular Signatures Database (MSigDB) collections v.5.2 that we […]


Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing

PMCID: 5879750
PMID: 29609564
DOI: 10.1186/s12903-018-0520-8

[…] enes database and the resulting KEGG orthologs table was then collapsed at level 3 of the KEGG annotations in order to display the inferred metabolic pathways. The resulting table was imported in the GAGE Bioconductor package [] to identify biological pathways overrepresented or underrepresented between PGs and RCs samples. To characterize the accuracy of PICRUSt, the Nearest Sequenced Taxon Index […]


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GAGE institution(s)
Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Bioinformatics Shared Resource, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Thermogenesis Corporation, Rancho Cordova, CA, USA; Department of Statistics, University of Michigan, Ann Arbor, MI, USA; Department of Animal Biology, University of Pennsylvania, Philadelphia, PA, USA; Bioinformatics Program, University of Michigan, Ann Arbor, MI, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
GAGE funding source(s)
Supported by NIH grant R01 DE017471; by NIH grant U54-DA-021519 and by NIH grants R01 AR054714 and R01 AR049682.

GAGE review

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Dr Nick

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A fairly easy algorithm and R package to perform custom gene set enrichment analyses with normalized expression datasets. My only qualm is the lack of information and examples to assist in the guidance of variable universe sizes among different datasets. A Fisher's test is very explicit in the effects of a changing universe size, but have had to empirically test, through numerous iterations, the equivalency of one sets enrichment results to another using the same reference set for comparison. Regardless, the ease of implementation compared with other popular packages, such as GSEA, make it possible to iteratively test such parameter changes in short order.