Question: GSEA for organisms with no GO terms?
0
gravatar for peter pfand
2.0 years ago by
peter pfand70
Germany
peter pfand70 wrote:

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.

go gsea • 695 views
ADD COMMENTlink modified 18 months ago by anne.de.jong0 • written 2.0 years ago by peter pfand70
0
gravatar for vchris_ngs
2.0 years ago by
vchris_ngs4.5k
Seattle,WA, USA
vchris_ngs4.5k wrote:

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.

ADD COMMENTlink written 2.0 years ago by vchris_ngs4.5k

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

ADD REPLYlink modified 24 months ago • written 24 months ago by peter pfand70

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.

ADD REPLYlink written 24 months ago by vchris_ngs4.5k
0
gravatar for anne.de.jong
18 months ago by
anne.de.jong0 wrote:

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

ADD COMMENTlink written 18 months ago by anne.de.jong0
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