blast2go testing for enrichment of GO terms

Question

[sm15766]

I am trying to see whether my differentially expressed genes are enriched for any particular GO terms. I've blasted, annotated and mapped all of my differentially expressed genes, but I I think I also need the GO terms from the rest of the genes in the genome as some kind of background comparison. I also have a .txt.annot file with the gene names and the Go terms in, but I'm not sure now to do the fishers exact test to test for enrichment. What format do the files need to be in?

Thanks

Answer 1

[dago]

You might be interested in reading older posts:

• GO Enrichment Analysis representation
• GO Term Enrichment Tutorial/Guide?
• Recommend Some Software/Package For Go Enrichment & Visualization
• GO enrichment in non-model organism

Or just type in "GO enrichment" in the search function in Biostars.

Good luck!

Answer 2

[EagleEye]

Try GeneSCF v1.0 with your custom annotation file,

A: GO enrichment analysis using a Text file with all the genes and GO ids associat