Toward a gold standard for benchmarking gene set enrichment analysis

Revision as of 15:38, 25 February 2020 by Ckreutz (talk | contribs) (Created page with "__ NUMBEREDHEADINGS__ === Citation === Geistlinger, L., Csaba, G., Santarelli, M., Ramos, M., Schiffer, L., Law, C., ... & Zimmer, R., Toward a gold standard for benchmarking...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

__ NUMBEREDHEADINGS__

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

Permanent link to the paper


Summary

Briefly describe the scope of the paper, i.e. the field of research and/or application.

Study outcomes

List the paper results concerning method comparison and benchmarking:

Outcome O1

The performance of ...

Outcome O1 is presented as Figure X in the original publication.

Outcome O2

...

Outcome O2 is presented as Figure X in the original publication.

Outcome On

...

Outcome On is presented as Figure X in the original publication.

Further outcomes

If intended, you can add further outcomes here.


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

  • The outcome was generated for ...
  • Configuration parameters were chosen ...
  • ...

Design for Outcome O2

  • The outcome was generated for ...
  • Configuration parameters were chosen ...
  • ...

...

Design for Outcome O

  • The outcome was generated for ...
  • Configuration parameters were chosen ...
  • ...

Further comments and aspects

References

The list of cited or related literature is placed here.