Question: Not clustered terms in david ontology functional annotation clustering
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gravatar for iraia.munoa
8 months ago by
iraia.munoa70
iraia.munoa70 wrote:

Hi everybody, I am using david ontology functional annotation clustering. The thing is that it results very few biological function groups and in the bottom of the page there is a a square saying " 54 terms were not clustered". What does it mean? I guess that the functional annotation clustering only gives as a result the gene ontology terms that can be clustered together, and in that square of not clustered terms there are the rest of the terms, that can't be match together.

So taken this in to account, would it be correct to use the functional annotation chart, to have all the information about the gene ontology terms, then use "revigo" or something like that to group the terms? Or I only can work with the few clustered terms?

Furthermore, does anyone use a specific tool to do the gene ontology annotation or annotation clustering with few genes? or another way to study their biological function when working with small batch of genes?

Thanks in advance,

Iraia

ADD COMMENTlink modified 8 months ago by Kevin Blighe49k • written 8 months ago by iraia.munoa70
1
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe49k
Kevin Blighe49k wrote:

Hi Iraia,

Your interpretation is correct. That is, the Functional Annotation Clustering first performs gene enrichment and tries to cluster the enriched terms into functional clusters. You can also just use the Functional Annotation Chart.

For Gene Ontology enrichment, I use topGO.

I do not mean to be patronising, but, if you just have a few genes of interest, then you could simply do a literature search and essentially do the 'enrichment' manually. For example, if my genes of interest were VSX1 and TGFBI, and my disease of interest was corneal dystrophy, then I would go to my search engine and search for:

  • ncbi "corneal dystrophy" TGFBI
  • ncbi "corneal dystrophy" VSX1

Kevin

ADD COMMENTlink written 8 months ago by Kevin Blighe49k
1

Ok, thanks Kevin. It was more a thing of understanding correctly the way David works, as I did not find anything about it in their manual. Thanks!!

ADD REPLYlink written 8 months ago by iraia.munoa70
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