Gene Family Member

Question

[bioinformatics123]

Is there any way to automate searching for gene family members? Checking gene members using genecards help but doing it manually for many genes is a problem. Is there any way to automate it using perl or R?

[Pierre Lindenbaum]

What do you mean with "family members" ?

[bioinformatics123]

For example, for a gene ITGA7 integrin, alpha7 other member would be ITGA9,ITGA10,ITGA2B,ITGAD etc..

Answer 1

[Pierre Lindenbaum]

using your exemple, you could use Gene Ontology Annotation for "integrin complex"

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008305#term=annotation

[bioinformatics123]

Thanks Pierre. ...But then it includes the uncharacterised protein aswell..for ex: itgb6 is
Integrin alpha 6 and Putative uncharacterized protein aswell..also, if it is itgb6 I assume its not for human but then shouldn't there be an entry for ITGB6? I was thinking more in terms of some kind of scripts that would input a gene name and output out all the gene family members. Is there any data out there that can be downloaded and used in such a pipeline?

Answer 2

[Malachi Griffith]

You should be able to obtain gene families using the Ensembl compara database. The documentation describes the methods used to define gene families. To automate you can use the Compara API which has a tutorial that describes some of the objects that might be useful to you. For example, from the tutorial:

"Typically you want to get homologies for a given gene. The HomologyAdaptor has a fetching method called fetchallby_Member(). You will need the Member object for your query gene, therefore you will fetch the Member object. In case of homology it is a gene, in case of family it can be a gene or a protein."

my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'Member');
my $member = $member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','ENSG00000004059');

"Then you get the homologies where the member is involved"

my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi', 'compara', 'Homology');
my $homologies = $homology_adaptor->fetch_all_by_Member($member);

"That will return a reference to an array with all homologies (orthologues in other species and paralogues in the same one). Then for each homology, you can get all the Members implicated." The docs go on to explain how you identify the subset of homologies that are paralogues...

[bioinformatics123]

Thanks! I am going through the documentation and tutorial.