Questions on subcellular location and species

Hello,

I have two questions on the “Targets” dataset (listed below) and would appreciate any insights anyone may have! Thanks.

  1. Why is a subcellular location included for every entry separate from a Cellular Component GO term?

  2. Are all of the entries (genes, targets) human-specific? I noticed that for every entry there was a “Species” specification, it seemed to fall under the “Homolog” category, and I was wondering if someone could explain to me if species is indeed listed under Homolog and what this means. I would just like to obtain human targets.

Hi teekay,

  1. Why is a subcellular location included for every entry separate from a Cellular Component GO term?

At the moment, subcellular location does not include the Gene Ontology Cellular Component data, which you can find in the Gene Ontology (GO) widget. There are differences in the way information is curated in Uniprot and HPA as opposed to GO. The most important difference is that GO does not aim to assess what’s the likely location of a particular gene product. Instead, it reports any evidence of the gene product being located in a particular subsystem. Some unlikely locations can occur as a consequence of this as discussed in previous posts.

  1. Are all of the entries (genes, targets) human-specific? I noticed that for every entry there was a “Species” specification, it seemed to fall under the “Homolog” category, and I was wondering if someone could explain to me if species is indeed listed under Homolog and what this means. I would just like to obtain human targets.

All entries in the targets dataset are human genes as described in the documentation. In the Homolog column you can find comparative genomics information retrieved from Ensembl Compara. This information will only be useful in case you want to find targets in other species with the same evolutionary origin as your human target.

I hope this helps

David

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