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The Molecular Signatures Database (MSigDB) hallmark gene set collection.

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Affiliations

  • 1. Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.
      Authors
    • Liberzon A 1
    • Birger C 1
    • Thorvaldsdóttir H 1
    • Ghandi M 1
    (4 authors)
  • 2. Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA; Department of Medicine, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92093, USA.
      Authors
    • Mesirov JP 2
    (1 author)
  • 3. Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA; Department of Medicine, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.
      Authors
    • Tamayo P 3
    (1 author)

Cell Systems, 01 Dec 2015, 1(6):417-425
https://doi.org/10.1016/j.cels.2015.12.004 PMID: 26771021 PMCID: PMC4707969

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Abstract 

The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.

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Read article at publisher's site: https://doi.org/10.1016/j.cels.2015.12.004

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    Funding 

    Funders who supported this work.

    NCI NIH HHS (3)

    • Grant ID: R01 CA121941

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    • Grant ID: U54 CA112962

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    • Grant ID: R01 CA154480

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    NIGMS NIH HHS (1)

    • Grant ID: R01 GM074024

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