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Extending support for mouse data in the Molecular Signatures Database (MSigDB)

Nature Methods volume 20, pages 1619–1620 (2023)Cite this article

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The rise of full transcriptome acquisition technologies has fueled the rapid proliferation of molecular-level biological data. These large datasets require interpretation beyond the single-gene level to connect them to meaningful biology and clinical impacts. In 2003, we pioneered the gene set enrichment analysis (GSEA) approach1 to enable the identification of the coordinate activation or repression of sets of genes that share common biology, thereby distinguishing even subtle differences between phenotypes or cellular states. We first released our GSEA software and a companion resource of gene sets, the Molecular Signatures Database (MSigDB), in 2005 (ref. 2).

Historically, the GSEA/MSigDB resource (https://gsea-msigdb.org) focused on the analysis of human-specific datasets. The gene sets in MSigDB were offered exclusively in the human gene space, and analysis of mouse data was minimally supported through basic ortholog mapping to human genes. In recognition of the importance of model organisms, particularly mice, for research into the mechanisms of human disease, we recently expanded the MSigDB to address this by introducing a database of mouse-native gene sets and by substantially improving MSigDB’s ortholog mapping.

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Fig. 1: Home page of the MSigDB resource.

Data availability

The MSigDB resource, including both mouse and human gene sets, is freely available at http://msigdb.org. The full GSEA/MSigDB resource is available at http://gsea-msigdb.org.

Code availability

The GSEA software is open source under a BSD-style license; the source code is available at http://github.com/GSEA-MSigDB. MSigDB is available under a Creative Commons license. The full license terms can be found at http://gsea-msigdb.org.

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Acknowledgements

This work was supported by US National Institutes of Health grant U24CA220341 to J.P.M.

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Author notes

  1. Deceased: Jill M. Recla.

Authors and Affiliations

  1. Department of Medicine, University of California San Diego, La Jolla, CA, USA

    Anthony S. Castanza, David Eby & Jill P. Mesirov

  2. The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME, USA

    Jill M. Recla & Carol J. Bult

  3. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Helga Thorvaldsdóttir

  4. Moores Cancer Center, University of California San Diego, La Jolla, CA, USA

    Jill P. Mesirov

Authors
  1. Anthony S. Castanza
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  2. Jill M. Recla
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  3. David Eby
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  5. Carol J. Bult
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Contributions

A.S.C. and J.M.R. developed the ortholog mapping procedure. C.J.B. and J.M.R. identified and curated the gene sets in the MP:Tumor collection; J.M.R. wrote the code to generate the gene sets. J.M.R. and C.J.B. produced the ortholog translated hallmarks collection. D.E. collected existing mouse gene sets from MSigDB. A.S.C. curated all other sets and collections and produced the underlying gene mapping data. A.S.C. and D.E. produced the complete MSigDB build. A.S.C., D.E. and H.T. designed the updates to the MSigDB website; D.E. implemented the updates. A.S.C., H.T. and J.P.M. wrote the manuscript with input and feedback from all authors. C.J.B. and J.P.M. provided oversight and guidance.

Corresponding author

Correspondence to Jill P. Mesirov.

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The authors declare no competing interests.

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Nature Methods thanks Jüri Reimand and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Notes 1–5, References and Figs. 1–2

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Supplementary Table 1

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Castanza, A.S., Recla, J.M., Eby, D. et al. Extending support for mouse data in the Molecular Signatures Database (MSigDB). Nat Methods 20, 1619–1620 (2023). https://doi.org/10.1038/s41592-023-02014-7

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