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GO question

Mary Dolan Mary_Dolan at umit.maine.edu
Thu Jun 24 14:15:40 PDT 2004


Antony Rodriguez <ar3 at sanger.ac.uk> writes:
>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.

Anthony,
Joel Richardson here at jax has a web tool that might do what you are asking for. 
VLAD - VisuaL Annotation Display - is a tool for visualizing GO annotations. The annotation data are a subset of those available at the GO web site (MGI, RGD, Human, Flybase, SGD, or ZFIN). You specify an annotation data set and a set of genes, and
the tool will produce a graphical summary of the annotations indicating statistically significant (overrepresented) nodes.
http://proto.informatics.jax.org/prototypes/vlad/
Mary

Mary Dolan, Ph.D.
************************************
Bioinformatics Department, The Jackson Laboratory
NCGIA, Department of Spatial Information Science and Engineering, University of Maine
Boardman Hall 329
University of Maine
Orono, Maine 04469
207.581.2143
fax: 207.581.2206
mdolan at informatics.jax.org
mary_dolan at umit.maine.edu
************************************


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