what is the difference between gene set test analysis and gene set enrichment analysis?

Question

[manasa22.reddy]

What is the difference between gene set test analysis and gene set enrichment analysis?

Answer 1

[svlachavas]

Dear Manasa,

basically although these terminologies are a bit arbitary and context depending, naively speaking: generally, consider that gene set enrichment analysis, which is basically functional/enrichment analysis, includes various gene set testing analysis methodologies, like overepresentation analysis, GSEA, etc. There are some very useful papers or tutorials which you can check:

• http://bioconductor.org/help/course-materials/2013/EMBOBGI/GeneSetEnrichment.pdf
• http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375
• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134237/

(* also to mention, in some general descriptions, they have been used described the same thing and have the same interpretation)

Hope this helps,
Efstathios

Answer 2

[Giovanni M Dall'Olio]

I am not sure it is the official definition, but in general I use:

• gene set analysis: you have a list of genes (e.g. genes differentially expressed in case vs controls), and you want to know the terms enriched
• gene set enrichment analysis (GSEA): instead of using only the genes that are differentially expressed, you use all the genes analysed, ranked by their expression ratio or by any ranking score, and you get a list of terms enriched in all genes weighting their ranks.