GSEA for organisms with no GO terms?

Question

[Juan Cordero]

I would like to perform a gene-set enrichment analysis in GO terms for the bacteria Acinetobacter baumannii, but I have looked at http://geneontology.org/ and there's no entry for it.

I would be very grateful if someone could tell me a way to see if any function is enriched from the differentially expressed genes I got from my experiments with A. baumannii.

Answer 1

[ivivek_ngs]

Take a look at this link to see what is available for GSEA tool by broad for GO terms.

Alternatively you have also take a look into this

The thing is still not clear about your motivation. Usually one does GO enrichment and that will have some sort of enrichment scores based upon the knowledge base and your input gene list. Then you can select the top GO terms based on some threshold of pvalue and enrichment association score. Why do you want to do again GSEA of GO terms. What you can do is taking a GO terms and the genes that you have in your list for that GO term and then perform classical GSEA for the specific molecular function of biological process. That will still give some kind of idea.

[Juan Cordero]

I want to perform a typical GO analysis, but I don't see any GO terms for my model (A. baumannii). I've found out proteins for this model do have a GO term in the UniProt Web, but it is inferred from electronic annotation, so I don't know how to continue/start with the GO analysis if I don't have a database for my model.

Thanks

[ivivek_ngs]

There is this publication which claims to work on the gene expression profile and they used BLAST2GO

There is another website BioCyc which you can take a look for GO on A. baumannii . May be this might be of some help.

Answer 2

[anne.de.jong]

For bacteria classes of GO, KEGG, PFAM, COG, PFAM, SMART, Superfamily, KEYWORDS and OPERONS http://genome2d.molgenrug.nl/index.php/functional-analysis-go-ipr