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New GO tools for analysing yeast gene/proteins

Bernard jacq at lgpd.univ-mrs.fr
Wed Jan 26 05:32:33 EST 2005

Dear colleagues,

This short mail to inform the yeast community of the availability of
GOToolBox, a series of programs using Gene ontology that we published
recently in Genome biology


The programs from GOToolBox are directly accessible through a Web site
described in the article.  They can be useful to analyse groups of
genes derived from microarrays,Chromatin-Immunoprecipitations, from
the analysis of protein-protein, protein_DNA and/or genetic networks, ...

GOToolBox performs five main tasks:

 - gene dataset creation,
 - selection and fitting of GO terms at a given ontology level (GO-Diet),
 - statistical analysis of GO terms associated with gene sets=20
   (GO-Stats) in order to find over- or under-represented terms,
 - GO-based gene clustering (GO-Proxy) allowing to find sub-groups of=20
   functionnally related genes within a gene set,
 - gene retrieval based on GO annotation similarity (GO-Family) in=20
   one or several species.

Other developments are presently on their way.  At the moment,
GOToolBox supports analyses of GO terms for six species : Yeast (Sc),
Arabidopsis, Drosophila, nematode, mouse and humans.

We also want to inform the yeast community that we will be releasing
(late march) datasets of direct protein-protein interactions (PPIs) in
yeast that we gathered from the literature. These interactions, that
we use to study the yeast PPI network, complement data that can be
found in the MIPS, DIP, BIND or GRID databases since a few hundreds of
interactions that we list are not present in other databases. These
data will be available as hypertext tables with PubMed links and also
in text format. It is anticipated that the first version of our
dataset will contain approximately 4500 to 5000 direct PPIs. We plan
to update this site every two or three months.  We will inform the
community as soon as this resource is available.

For the authors,

David Martin and Bernard Jacq

Bernard Jacq
Parc Scientifique de luminy
13288 Marseille Cedex 9

tel (33) 04 91 82 94 25
fax (33) 04 91 82 06 82

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de GRENOBLE, continuez =E0 d=E9fendre la recherche=20
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