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Drawing GO hierarchical trees

Mary Dolan Mary_Dolan at umit.maine.edu
Tue Jun 22 07:59:48 PDT 2004


>Hi!
>
>Given a list of GO-ids belonging to any one category
>(processs,function,component), is there an easy way to draw the (HTML)
>hierarchical tree for those terms? 
>
>I need to draw a tree (using a perl script) for GO terms deemed
>'significant' for a group of genes. We have a local installation of GO to
>get the parents of each term and I was wondering if there is a module out
>there that would let me draw the trees without reinventing the wheel. I am
>sure people must have done this many times before. So if some one can
>provide tips/perl code/modules to do that it would be fabulous. Thanks in
>advance!
>
>Regards,
>Nigam Shah.
>
>Nigam Shah
>Graduate Fellow, 
>Huck Institute for Life Sciences,
>Penn State University.
>Ph:(814)863-5720
>Web: www.personal.psu.edu/nhs109/


Hi, Nigam.
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/

If your genes are from another organism, you can use Gavin Sherlock's generic GO TermFinder, which has a GO graphical display function.
http://search.cpan.org/dist/GO-TermFinder/

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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