Toward a gold standard for benchmarking gene set enrichment analysis

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Citation

Geistlinger, L., Csaba, G., Santarelli, M., Ramos, M., Schiffer, L., Law, C., ... & Zimmer, R., Toward a gold standard for benchmarking gene set enrichment analysis, 2020, Bioinformatics, 0, 1-12

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Summary

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Study outcomes

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Outcome O1

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Outcome O2

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Outcome On

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Further outcomes

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Study design and evidence level

General aspects

  • "75 expression datasets investigating 42 human diseases"
  • microarray and RNAseq data
  • pre-existing benchmark data sets
  • 10 methods:
    • ORA
    • GLOBALTEST
    • GSEA
    • SAFE
    • GSA
    • SAMGS
    • ROAST
    • CAMERA
    • PADOG
    • GSVA
  • "Gene set relevance rankings for each disease were constructed by querying the MalaCards database. MalaCards scores genes for disease relevance based on experimental evidence and co-citation in the literature."

Design for Outcome O1

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Design for Outcome O2

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Design for Outcome O

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Further comments and aspects

References

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