Question: GO Term enrichment prokaryotes
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ksw • 40 wrote:
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?
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Sukhdeep Singh ♦ 10.0k wrote:
Not a lot is out there regarding gene set enrichment in Prokaryotes.
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
0
anne.de.jong • 0 wrote:
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
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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,