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Author Topic:   new gene ontology software for biomedical research Cc:
posted 03-03-2005 09:16 PM     Click Here to See the Profile for jacq     Edit/Delete Message Reply w/Quote
Dear colleagues,

This short mail to inform the community of people involved in biomedical research 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).

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, ....
In the area of biomedical research, the GOToolbox suite can potentially be useful for people involved in microarray or proteomic research and who want to make functional sense of groups of genes identified using these high throughput approaches.

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


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