I would like to retrieve a list of all the human genes and their proteins’ functional classification.
Gene type attribute on ensembl.org is not specific enough, because it assign the label
coding protein to all the proteins for which I am trying to classify. Also the
KEGG Pathway and Enzyme ID option doesn't seem to help.
I have translated all the gene names to their GO representation, but now I am not sure how to query for their cellular function, biological process, and cellular component.
Is there such a platform that can retrieve this info from PANTHER?
Sadly, the reference proteome of humans doesn't contain a functional classification either:
zcat UP000005640_9606.fasta.gz | grep -i mYOSIN-2 >sp|Q9UKX2|MYH2_HUMAN Myosin-2 OS=Homo sapiens OX=9606 GN=MYH2 PE=1 SV=1 # >db|UniqueIdentifier|EntryName ProteinName OS=OrganismName OX=OrganismIdentifier [GN=GeneName ]PE=ProteinExistence SV=SequenceVersion
I think that getting the most specific (
GO term name) and least specific (
GO domain) gene's GO values can be retrieved from ensmebl: