Question: GO Term enrichment prokaryotes
3
gravatar for ksw
3.9 years ago by
ksw40
United States
ksw40 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?

prokaryote go enrichment • 1.9k views
ADD COMMENTlink modified 2.4 years ago by anne.de.jong0 • written 3.9 years ago by ksw40

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,

ADD REPLYlink written 3.9 years ago by ksw40
2
gravatar for Sukhdeep Singh
3.9 years ago by
Sukhdeep Singh9.8k
Netherlands
Sukhdeep Singh9.8k 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

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Sukhdeep Singh9.8k
0
gravatar for anne.de.jong
2.4 years ago by
anne.de.jong0 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

ADD COMMENTlink written 2.4 years ago by anne.de.jong0
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