GO annotation for genes unkown by Panther and Reactome
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7.0 years ago
biocyberman ▴ 840

I searched Panther database and Reactome database in order to annotate my list of genes with functional information. My list is about 600 genes, and both databases can find only about 200 genes. What tools can I use to annotate 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 • 1.6k views
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7.0 years ago
Benn 8.3k

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.

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7.0 years ago
Girolamo ▴ 140

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
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7.0 years ago

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

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