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[go-friends] GO gene set for all the children of a GO

Rama Balakrishnan ramab at stanford.edu
Fri Aug 9 09:31:33 PDT 2013


Ari,

You can use GOOSE to do this kind of query. Here is how-
1) Go to: http://berkeleybop.org/goose

2) Type in the following query in the text box. I have put some random GO term names in the last line of this query (term.name in ('reproduction')). Please fill in the term names of your interest. They have to be placed within single quotes. Also, increase the limit of the number of results returned to 'unlimited' using the pull down option.

SELECT
 term.name AS superterm_name,
 term.acc AS superterm_acc,
 term.term_type AS superterm_type,
 association.*,
 gene_product.symbol AS gp_symbol,
 gene_product.symbol AS gp_full_name,
 dbxref.xref_dbname AS gp_dbname,
 dbxref.xref_key AS gp_acc,
 species.genus,
 species.species,
 species.ncbi_taxa_id,
 species.common_name
FROM term
 INNER JOIN graph_path ON (term.id=graph_path.term1_id)
 INNER JOIN association ON (graph_path.term2_id=association.term_id)
 INNER JOIN gene_product ON (association.gene_product_id=gene_product.id)
 INNER JOIN species ON (gene_product.species_id=species.id)
 INNER JOIN dbxref ON (gene_product.dbxref_id=dbxref.id)
WHERE
species.genus = 'Drosophila'
and term.name in ('reproduction', 'nucleus', 'translation');

Please let us know if you have questions.

Best,

Rama



On Aug 8, 2013, at 6:27 AM, Ari Eszter wrote:

> Dear GO Friends,
> 
> I would like to create a GO annotation text file which contains the set of genes connected to each GOids and its all descendants (children, grandchildren, etc.).
> 
> For example in GO:0000003 "reproduction" would contain ALL the genes which can be connected to reproduction and its all descendants, not only the genes which can be connected to this term exclusively but not to its descendants.
> 
> Therefore it would be a union of all genes that involved in reproduction and its descendants terms. (And the same for every GOid.)
> 
> Like in the association file of Funassociate: http://llama.mshri.on.ca/funcassociate/download_go_associations
> 
> Can somebody give me some hints how to do this?
> (I am working with D.melanogaster and FlyBase geneIDs - FBgn)
> 
> It would be also a great help if I would be able to solve to have all the descendants (children, grandchildren...) for each GOids.
> 
> Many thanks,
> Eszter
> 
> -- 
> Eszter Ari
> Institut für Populationsgenetik
> Vetmeduni Vienna
> Veterinärplatz 1
> 1210 Wien, Austria
> _______________________________________________
> go-friends mailing list
> go-friends at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/go-friends



=============================
Rama Balakrishnan
GO Curator (www.geneontology.org)
SGD Curator (www.yeastgenome.org)
=============================

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