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

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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.

References

  1. Mootha, V. K. et al. Nat. Genet. 34, 267–273 (2003).

    Article  CAS  PubMed  Google Scholar 

  2. Subramanian, A. et al. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Liberzon, A. et al. Cell Syst. 1, 417–425 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Alliance of Genome Resources Consortium. Genetics 213, 1189–1196 (2019).

    Article  Google Scholar 

  5. Hu, Y. et al. BMC Bioinformatics 12, 357 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Herrero, J. et al. Database (Oxford) 2016, baw053 (2016).

    Article  PubMed  Google Scholar 

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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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  4. Helga Thorvaldsdóttir
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  5. Carol J. Bult
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  6. Jill P. Mesirov
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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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Competing interests

The authors declare no competing interests.

Peer review

Peer review information

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

Supplementary Table

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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  • DOI: https://doi.org/10.1038/s41592-023-02014-7

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