I've downloaded the gene_association.goa_human file from the ebi website. I tried running a python script to filter out GO IDs with "membrane" in the description. This approach doesn't seem to be working because the target receptor I am looking for doesn't contain "membrane" in the description ( though it is a membrane receptor). The QuickGo search feature on the ebi website using the GO id corresponding to the target receptor, however, gives me the correct description in the name field ( name : membrane ). Is there anyway I can get a list of human GO ID's that contain the appropriate descriptions ( the gene_assocation.goa_human file doesn't work ). My aim is to generate a list of GO ID's and Gene names that correspond to membrane expressed proteins.
Appreciate any help
You can easily generate a list of all human membrane-associated genes using the web service AmiGO2 (Gene Ontology).
- Search for a GO record of membrane as a cellular component. I think the accession number is GO:0016020.
- In the Associations tab, filter protein products according to a given taxon (Homo sapiens) and source database (e.g. UniProt, Ensembl, RefSeq etc.).
- Download the resulting list choosing a format that suits you (e.g. tab-separated file, sequences in FASTA format).
For example, here's a list of all gene products related to membrane.