Question: what is the difference between gene set test analysis and gene set enrichment analysis?
2
gravatar for manasa22.reddy
2.7 years ago by
United States
manasa22.reddy40 wrote:

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

microarray analysis forum • 2.3k views
ADD COMMENTlink modified 2.7 years ago by Giovanni M Dall'Olio26k • written 2.7 years ago by manasa22.reddy40
3
gravatar for svlachavas
2.7 years ago by
svlachavas450
Greece
svlachavas450 wrote:

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

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by svlachavas450
3
gravatar for Giovanni M Dall'Olio
2.7 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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.
ADD COMMENTlink written 2.7 years ago by Giovanni M Dall'Olio26k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 987 users visited in the last hour