New GO tools for analysing drosophila gene/proteins

Bernard jacq at ibdm.univ-mrs.fr
Sat Jan 22 19:50:03 EST 2005



 Dear colleagues,

 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 
(http://www.biomedcentral.com/content/pdf/gb-2004-5-12-r101.pdf).

 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 
network.

 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)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&d 
opt=Abstract&list_uids=14605208

 - Stanyon CA, .... Finley RL (Genome biology, 2004) 
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&d 
opt=Abstract&list_uids=15575970

 - 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


Bernard Jacq
LGPD-IBDM
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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