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GO question

Dopazo.Joaquin jdopazo at cnio.es
Fri Jun 25 01:56:35 PDT 2004


Dear Antony,
You can have a look to FatiGO (http://fatigo.bioinfo.cnio.es) (see Al-Shahrour et al., 2004, Bioinformatics 20,578-580).
You can test if the proportions in differenjt GO terms are really significantly different. FatiGO uses FDR or FWER to adjust the p-values since you are testing simultaneously hundreds of terms, which causes a high number of false positives. You can find more information at our web site.
If you need some further help do not hesitate in contacting me.
Yours
Joaquin

Joaquin Dopazo
Head of Bioinformatics, 
Centro Nacional de Investigaciones Oncologicas
c/ Melchor Fernandez Almagro 3. 
28029, Madrid, Spain.

Tf. (+34) 912246919
Fax (+34) 912246972
http://bioinfo.cnio.es
 

> -----Mensaje original-----
> De: Antony Rodriguez [mailto:ar3 at sanger.ac.uk]
> Enviado el: jueves, 24 de junio de 2004 22:09
> Para: gofriends at genome.stanford.edu
> Asunto: GO question
> 
> 
> Dear GO members,
> 
> I came accross the GO website and wanted to ask you guys a specific 
> question.
> 
> I have a small set of genes from humans (approx 200) and I retrieved 
> biological processes and molecular functions for each one.  
> My question 
> is, how or where do I go to compare the frequency 
> (abundances) for each 
> category within this group with that of the entire genome as 
> a whole?  
> For instance if in this set there are 20 out of 200 genes with a 
> 'transport' GO:0006810 biological process and I wanted to 
> determine if 
> this is unusually high fraction within my sample size as compared to 
> the total fraction of 'transport' genes in the entire human genome 
> where would I search for such information?
> 
> Thanks for the help,
> 
> Antony Rodriguez, Ph.D.
> Fellow
> Mouse Genomics Team 82
> Wellcome Trust Sanger Institute
> Genome Campus
> Cambridge CB10 1SA  UK
> tel: 44-1223-834244 Ext: 7165
> FED EX ACCT: 1650 94344
> 
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