Gene Ontology Analysis...

Question

[Manish]

hello frnds.. i m new in this field. can anybody tell me what is exact meaning of fold enrichment and what can we find out by knowing this? thanks you.

[Khader Shameer]

Basic aspects of gene ontology enrichment analysis are discussed here.

[Manish]

thanks for suggestion.

Answer 1

[Madelaine Gogol]

You could possibly be talking about Fold enrichment in terms of:

number of genes found in list X with a certain GO term

divided by

number of genes expected (based on size of list and number of genes in genome with GO term)

A lot of times people do a hypergeometric or fisher's exact test to find significantly enriched GO terms, then make a plot or table listing the fold enrichment for each term.

[Madelaine Gogol]

That would mean that you have 3 times as many genes annotated with that term as you would expect given the size of your gene list and the number of genes annotated with that term in the genome.

[Manish]

thanks for nice response..now i got what is fold enrichment. plz tell me, if i get 3 fold enrichment for particular GO term, what does it mean? thank you..

[Manish]

thank you again

Answer 2

[Chris Evelo]

Where did you stumble on that term? It is indeed not very clear.

Since you mention gene-ontology in the title and tags you are probably looking at methods that look for enrichment of genes that meet a certain condition and to a specific GO term. That condition in gene expression experiments will often be a fold change.

[Manish]

thanks for answer sir.