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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References

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