Gene Networks Validation based on Metabolic Pathways

Abstract

In the last few years, DNA microarray technology has attained a very important role in biological and biomedical research. It enables analyzing the relations among thousands of genes simultaneously, generating huge amounts of data. The gene networks represent, in a graph data structure, genes or gene products and the functional relationships between them. These models have been fully used in Bioinformatics because they provide an easy way to understand gene expression regulation. Nowadays, a lot of gene network algorithms have been developed as knowledge extraction techniques. A very important task in all these studies is to assure the network models reliability in order to prove that the methods used are precise. This validation process can be carried out by using the inherent information of the input data or by using public biological knowledge. In this last case, these sources of information provide a great opportunity of verifying the biological soundness of the generated networks. In this work, authors present a gene network validation methodology based on the information stored in KEGG database. With this aim, a complete KEGG pathway conversion to gene network is presented, and a global and functional validation process is proposed, where the whole metabolical information stored in KEGG is used at the same time.