GO enrichment analysis for pseudogenes in bacterium

Question

[mschmid]

I would like to check for pseudogenes of a bacterium if I find some groups of genes beeing more present than others. I would like to do that via GO terms. I already have the GO numbers extracted using InterProScan against Pfam database.

How do I check if some enrichement is present? I would like to this for a Lactobacillus species.

If there is an Idea for another approach, I have the following information: 1. Complete annotation of the genome 2. All CDS sequences as DNA/AA 3. Pseudogenes as DNA and the six frame translations of this sequence (meaning that at least one of this translations give a meaningfull result when compared to a database)

Any Ideas?

UPDATE: Now I have all the GO numbers (in format like GO:0016021) for the pseudogenes and also for all CDS (as the background). Do you know some tools beeing able to deal with this to perform enrichment analysis?

Answer 1

[dago]

There have been quite a few similar question in bioastars:

GO enrichment analysis on Non-model Organism

GO Term enrichment prokaryotes

How can I do GO enrichment analysis for bacteria genome? (biomaRt is not support bacteria anymore)

I personally prefer topGO or GOstat, in bioconductor, but there are many other packages available. Check the section gene set enrichment in Bioconductor. An alternative would be Bingo on Cytoscape. Hope this helps.