New Gene Ontology tools/DNA binding &

Bernard jacq at
Wed Mar 2 03:48:12 EST 2005

This short mail to inform the community of
researchers interested in 
 chromatin structure and function 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.
  GOToolBox can be useful to analyse groups of genes
 derived from 
 microarrays,Chromatin-Immunoprecipitations, from the
 analysis of 
 protein-protein (two-hybrid), protein_DNA and/or
 genetic networks.
  In the context of chromatin structure and function
 GOToolBox can be particularly usful to analyse the
 results of ChIP or 
 ChIP-chip experiments, or more generally to examine
 functional links 
 existing between targets of Chromatin/DNA binding
 proteins. the 
 GOToolBox suite can also be used, for instance, to
 analyse if 
 neighboring genes on chromosomes are functionnaly
  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 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.
  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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