GO Term enrichment prokaryotes

Question

[ksw]

I am new to gene ontology and was wondering the best tool to use to test if a gene set is enriched for certain GO terms in a non-model prokaryote?

[ksw]

Fantastic, thank you! I just found that DAVID is actually very flexible and allows for input of user generated gene and background lists. I will look through FINA and JProGo as well.

Cheers

Answer 1

[Sukhi Singh]

Not a lot is out there regarding gene set enrichment in Prokaryotes.

A few links that might be helpful and give you a push:

• How To Get The Gene Names To Go Terms For Bacteria And Archaea
• Why Is There Lack Of Go Terms With A Prokaryotic Genome.

An excerpt from Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615629/

Several enrichment tools were specifically designed for these less popular species, such as WEGO for rice (54); easyGO for crops (66); FINA for prokaryotes (58); CLENCH for Arabidopsis (21); JProGo for prokaryotes (48); BayGo for Xylella fastidiosa (52).

Protein Localization Analysis of Essential Genes in Prokaryotes

HTH

Answer 2

[anne.de.jong]

GSEA for GO KEGG, InterPro, COG, PFAM, SMART, Superfamily, KEYWORDS and OPERONS can be done for all complete genomes of the NCBI here: http://genome2d.molgenrug.nl/index.php/functional-analysis-go-ipr