New GO tools for analysing drosophila gene/proteins
jacq at ibdm.univ-mrs.fr
Sat Jan 22 19:50:03 EST 2005
This mail to inform the drosophila community of the availability of
GOToolBox, a series of programs using Gene ontology that we published
recently in Genome biology
GOToolBox will be useful to analyse Drosophila groups of genes
derived from microarrays, Chromatin-Immunoprecipitations, from the
analysis of protein-protein, protein_DNA and/or genetic networks, ....
The programs from GOToolBox are directly accessible through a Web
site described in the article.
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
(GO-Stats) in order to find over- or under-represented terms,
- GO-based gene clustering (GO-Proxy) allowing to find sub-groups of
functionnally related genes within a gene set,
- gene retrieval based on GO annotation similarity (GO-Family) in
one or several species.
Other developments on GOToolBox 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 drosophila community that we will be
releasing (late march) datasets of direct protein-protein
interactions (PPIs) in drosophila that we gathered from the
literature. We are using such data to analyse the drosophila PPI
Our collection, which relies mainly on small-scale data, complements
data that has been obtained in recent high-throughput 2H screens :
- Giot L, ..... Rothberg JM (Science, 2003)
- Stanyon CA, .... Finley RL (Genome biology, 2004)
- Formstecher E. ...... Daviet L (Genome Research, in press)
Our 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 1000 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
Parc Scientifique de luminy
13288 Marseille Cedex 9
tel (33) 04 91 82 94 25
fax (33) 04 91 82 06 82
Aprés les Etats généraux de la Recherche
de GRENOBLE, continuez à défendre la recherche
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