A general modular framework for gene set enrichment analysis

1 Citation

M Ackermann and K Strimmer, A general modular framework for gene set enrichment analysis, 2009, BMC Bioinformatics, 10:47, pages etc in any possible citation style.

Permanent link to the paper

2 Summary

Gene set analyses have a modular structure, i.e. they consist of

1. gene level statistics
2. gene level significance assessment
3. gene set statistics
4. gene set significance assessment
5. statistical conclusion

Alternatively, steps 1.-3. might be replaced by a single global test.

In this paper, 261 different variants of gene set enrichment procedures were evaluated based on simulated and experimental data.

3 Study outcomes

List the paper results concerning method comparison and benchmarking:

3.1 Outcome O1

The performance of ...

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

3.2 Outcome O2

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

3.3 Outcome On

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

3.4 Further outcomes

If intended, you can add further outcomes here.

4 Study design and evidence level

4.1 General aspects

• The simulated data sets have 600 features (genes) and 20 samples (10 vs. 10)
• The data was simulated with normally distributed noise with variance equals to one
• 520 genes were consided as uninformative (delta=0, rho=0)
• Gene sets with different levels of differential expression (delta \in {0, 0.75, 1, -1}) were simulated
• Gene sets with varying levels of intra-group correlation (rho \in {0, 0.6, -0.6}) were simulated
• Gene sets that contain regulated and unregulated genes were generated as well as gene set that contain up- and downregulated genes.

4.2 Design for Outcome O1

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

4.3 Design for Outcome O2

• The outcome was generated for ...
• Configuration parameters were chosen ...
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4.4 Design for Outcome O

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

The list of cited or related literature is placed here.