Combining biomedical knowledge and transcriptomic data to extract new knowledge on genes

Emilie Guérin and Gwenaëlle Marquet, Julie Chabalier, Marie-Bérengère Troadec, Christiane Guguen-Guillouzo, Olivier Loréal, Anita Burgun and Fouzia Moussouni

Correspondence should be addressed to:
Gwenaëlle Marquet
EA 3888, IFR 140, Université de Rennes 1, Faculté de Médecine, 35043 RENNES Cedex, France
rf.1senner-vinu@nullteuqram.elleanewg

Abstract

In biomedical research, interpretation of microarray data requires confrontation of data and knowledge from heterogeneous resources, either in the biomedical domain or in genomics, as well as restitution and analysis methods adapted to huge amounts of data. We present a combined approach that relies on two components: BioMeKE annotates sets of genes using biomedical GO and UMLS concepts, and GEDAW, a Gene Expression Data Warehouse, uses BioMeKE to enrich experimental results with biomedical concepts, thus performing complex analyses of expression measurements through analysis workflows. The strength of our approach has been demonstrated within the framework of analysis of data resulting from the liver transcriptome study. It allowed new genes potentially associated with liver diseases to be highlighted.

Reference

E. Guerin and G. Marquet, J. Chabalier, M.-B. Troadec, C. Guguen-Guillouzo, O. Loreal, A. Burgun and F. Moussouni. Combining biomedical knowledge and transcriptomic data to extract new knowledge on genes. Journal of Integrative Bioinformatics, 3(2):35, 2006. Online Journal: http://journal.imbio.de/index.php?paper_id=35