Question: GO annotation for genes unkown by Panther and Reactome
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gravatar for biocyberman
4.0 years ago by
biocyberman810
Denmark
biocyberman810 wrote:

I searched Panther database (http://pantherdb.org/geneListAnalysis.do) and Reactome database (http://www.reactome.org/) in order to annotate my list of genes with functional information. My list is about 600  genes, and both databse can find only about 200 genes. What tools can I use to annoate the rest of the list? I want to essentially do functional annotation for the genes with GO terms as many genes as possible.

gene ontology • 1.1k views
ADD COMMENTlink modified 4.0 years ago by Tanvir Ahamed 290 • written 4.0 years ago by biocyberman810
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gravatar for Benn
4.0 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

You can try GO.db in R, but I don't think you will find annotation for all your genes. Especially not if both panther and reactome give similar number of annotated genes.

ADD COMMENTlink written 4.0 years ago by Benn7.9k
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gravatar for Girolamo
4.0 years ago by
Girolamo140
Italia
Girolamo140 wrote:

could depend on two factors:

  • The level of annotation of your species (400 genes not annotated in home sapiens are quite a lot)
  • The id you are using. I highly recommend to use gene id, instead of gene names for example
ADD COMMENTlink written 4.0 years ago by Girolamo140
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gravatar for Tanvir Ahamed
4.0 years ago by
Sweden
Tanvir Ahamed 290 wrote:

If you have the sequences of rest 400, you can think about homology against any well annotated species (e.g. human )

ADD COMMENTlink written 4.0 years ago by Tanvir Ahamed 290
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