Question: Relation between GO terms of homologous genes in different organisms.
gravatar for zuhaibzulfiqarahmed
4 days ago by
zuhaibzulfiqarahmed0 wrote:


I'm writing a small program that takes in a list of Uniprot gene names (and organisms of interest), and returns a visual representation of the GO terms associated with that list of genes in the specified organisms. I've run into an issue though. What if Uniprot doesn't have the GO terms for a gene in the specified organism? It might have the GO terms for that gene in other organisms, but not the one specified. So I wanted to ask, could I take the GO terms from the organism in the search results, that's the closest relative to the one of interest? If so, how do I determine which organism is the closest? I'm not very familiar with any phylogenetic resources where I give it a list of organisms and it returns a phylogeny of those organisms. Or are there easier ways to get the GO terms?

I appreciate the help. Also, if I do end up releasing this software, how do I reference this website? Or do I reference a specific user whose answer I used?

ADD COMMENTlink written 4 days ago by zuhaibzulfiqarahmed0

Transferring annotations between orthologs is commonly done. You don't have to limit yourself to a closely related species but can transfer annotations from any ortholog. For example yeast and Drosophila annotations are routinely used to annotate human genes. Depending on which organisms you're dealing with, you can use Ensembl Compara as a source of ortholog relationships.

ADD REPLYlink written 4 days ago by Jean-Karim Heriche17k

@Jean-Karim Heriche Thanks for the reply. So for example, the mgsA gene in E coli would have similar annotations as the mgsA gene in humans?

ADD REPLYlink written 4 days ago by zuhaibzulfiqarahmed0

I wouldn't know without seeing a phylogenetic tree but I certainly wouldn't make the inference based on name. Also I don't think one can infer orthology for groups as distant as mammals and bacteria. If interested in bacterial genes then look for other bacterial species. But generally, this is the idea: given a list of orthologous genes in multiple species, one can pool the annotations so that the whole group shares the same annotations.

ADD REPLYlink written 4 days ago by Jean-Karim Heriche17k
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