Question: GSEA for organisms with no GO terms?
gravatar for peter pfand
2.6 years ago by
peter pfand80
peter pfand80 wrote:

I would like to perform a gene-set enrichment analysis in GO terms for the bacteria Acinetobacter baumannii, but I have looked at 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 • 868 views
ADD COMMENTlink modified 2.1 years ago by • written 2.6 years ago by peter pfand80
gravatar for ivivek_ngs
2.6 years ago by
Seattle,WA, USA
ivivek_ngs4.6k 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 2.6 years ago by ivivek_ngs4.6k

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.


ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by peter pfand80

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 2.6 years ago by ivivek_ngs4.6k
gravatar for
2.1 years ago by wrote:

For bacteria classes of GO, KEGG, PFAM, COG, PFAM, SMART, Superfamily, KEYWORDS and OPERONS

ADD COMMENTlink written 2.1 years ago by
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