[BiO BB] Extracting GeneNames from a GO class and their syblings

Gaj Stan (BIGCAT) Stan.Gaj at BIGCAT.unimaas.nl
Wed Nov 28 09:12:08 EST 2007

Dear all,


My question today concerns GeneOntology annotation extraction. Is it
possible to extract a list of genes which belong to a specific
GO-process and it's children?


Or, to put it in a more clearer context:


- I'm interested in all genes belonging to the Lipid Metabolic process
category (GO:0006629 : lipid metabolic process
w_associations=list>  ).

- I aim to have a list of ALL genes that belong to this GO category or
below, up untill the smallest, most specific node (i.e. cellular lipid
metabolic process
w_associations=list>   -> cellular lipid catabolic process
w_associations=list>   --> etc)

- This list can afterwards be filtered for duplicate names / IDs using
Perl or something similar (can do that part myself (-; )

- In the end, I would like to have a list that consists of gene names or
any other usable ID(i.e. like EnsEMBL, UniProt, EntrezGene, ...) which
are classfied as having a Lipid Metabolic activity!


Is there a specific GO-Tool available (or am I unaware that this is even
possible in GO itself) that can do this? If the solution presents itself
by using R and specific GO-libraries, then I'm eager to hear about it as
well (-: (since I know it is possible to extract both parent and
children nodes, but am unaware on how to do this for gene names/IDs).


Best wishes and thanks in advance,


  -- Stan Gaj

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