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question about GO

Cheng, Jill Jill_Cheng at affymetrix.com
Mon Jun 28 11:32:43 PDT 2004


I would highly recommend you check out Affymetrix's free tool "GO browser",
it returns a tree view of GO terms, this tree view is at the same time a
heat map, colored by the counts of gene hits on certain GO terms.  The
counting is sensitive to parent-child relationship, so when a gene hits a GO
term, the parent terms are also counted, so you can find a higher level
"hot" category under which many input genes are annotated by the children GO
terms.  

This is a nice free tool, very easy to use, it takes a input text file with
a list of Affy probe names or unigne id, locuslink id, etc.  you do need to
register with your email address.
It's a bit tricky to find the tool, once you registered, you can use this
link
https://www.affymetrix.com/analysis/netaffx/batch_query.affx

and under 4. Select a view
you should choose "*Annotation List*"
query will return a table with gene annotations, on top of the table, you
can choose "GO browser" for graphical display. 

Cheers
 
Jill Cheng, Ph.D. | Staff Bioinformatics Engineer | Affy Labs -
Transcriptome | AFFYMETRIX, INC. | 3380 Central Expressway | Santa
Clara, CA 95051 | Tel: 408-731-5310 | Fax: 408-481-0422




-----Original Message-----
From: Isabelle Janoueix [mailto:Isabelle.Janoueix at curie.fr]
Sent: Monday, June 28, 2004 7:51 AM
To: gofriends at genome.stanford.edu
Subject: question about GO


Hello,

We are interested in using Gene Ontology but we have troubles to 
perform the search as we would like. Përhaps, you could help us. We 
have a list of about 200 genes and we would like to search for 
potential links between these genes such as common cellular function, 
conserved functional domains...
Using amiGO, we could get a list of terms for a specific gene but we 
try an advanced query with several genes, it does not work : if we 
choose the "homo sapiens" database, we get a server error; if we 
choose "all databases" it works but we get all the homologs for each 
protein in all species and then we have to check only the homo 
sapiens proteins, which is quite long if we work with a list of more 
than 100 genes !

So, we wonder how to manage with our list of genes ?

We thank you very much in advance for your help and hope an answer soon,

Sincerely,

Isabelle Janoueix

-- 
Isabelle Janoueix-Lerosey, Ph. D.
Laboratoire de "Pathologie Moléculaire des Cancers"
INSERM U509
Institut Curie
Section de Recherche
Pavillon Trouillet-Rossignol
26, rue d'Ulm
75231 Paris Cedex 05
France
tel: (33-1) 42 34 66 84
fax: (33-1) 42 34 66 30
Email: janoueix at curie.fr


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This message is from the GOFriends moderated mailing list.  A list of public
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