How to carry out a gene set analysis using custom gene sets?
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SamGG ▴ 270
@samgg-6428
Last seen 5 weeks ago
France/Marseille/Inserm

Hi,

I would like to carry out a gene set enrichment analysis using gene sets designed by an expert (ie lists of carefully chosen genes). The tools are numerous and the turnover is fast. So I appreciate any clue.

Best.

gene set analysis • 3.3k views
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Your comment about "numerous tools" makes me wonder whether you are looking for an initial suggestion or whether you already know of a number of tools and want to choose between them? If the latter, then we'd need to know more about what tools you are considering and what you want to achieve in your study.

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@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia

We designed and use roast and barcodeplot (part of the limma package) for this specific purpose.

Here are some examples of use. Each of these papers includes at least one barcodeplot and accompanying roast test for a custom gene set:

 http://www.ncbi.nlm.nih.gov/pubmed/25973911 (figures 2 and 4)

 http://www.ncbi.nlm.nih.gov/pubmed/24939936 (figure 5)

 http://www.ncbi.nlm.nih.gov/pubmed/25605372 (figure 6)

 http://www.ncbi.nlm.nih.gov/pubmed/25655195 (figure 2)

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Thanks for the links.

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svlachavas ▴ 780
@svlachavas-7225
Last seen 8 weeks ago
Germany/Heidelberg/German Cancer Resear…

Dear Samuel,

the term "gene set" enrichment" is very general and it varies depending on the specific experimental design and the goals of your study, and also of the "kind" of the test you want to perform(i.e. hypergeometric, topology based, self-contained null linear models by mroast/roast etc.).

You can check the following review (http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375) and also the course material from bioconductor (http://bioconductor.org/help/course-materials/2013/EMBOBGI/GeneSetEnrichment.pdf), which adress in details the specific modules. Just to pinpoint, from personal experience and from literature, the Molecular Signatures Database from the Broad Institute has excellent and curated gene sets regarding various field(TFs, cancer etc)(http://www.broadinstitute.org/gsea/msigdb/collections.jsp#C6), as also the web-tool Enrichr (http://amp.pharm.mssm.edu/Enrichr/).

Best,

Efstathios

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I chose a general term purposely in order to get as many information as possible. Your given links are relevant. The MSIGDB is a good resource, but in order to reduce the multiple test correction, targeted or ad hoc geneset collection is valuable. The C6 might be an interesting compromise. C6 contains some curated signatures from publications. Nevertheless, IMHO, cancer signatures have a lot of common genes that puzzle the interpretation. Thanks for your comment and the links, especially Enrichr which is very rich.

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Well, it depends on your experimental analysis and study goals. Anyway, from MSIGDB you could subset a general category to include only some releveant parts(for instance for C2, you could keep only to test for the KEGG pathways).

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