GO Term enrichment prokaryotes
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6.3 years ago
ksw ▴ 40

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?

GO enrichment prokaryote • 3.1k views
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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,

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6.3 years ago

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

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4.9 years ago
anne.de.jong ▴ 10

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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