ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato.

Co-expressed genes are often expected to be functionally related and many bioinformatics approaches based on co-expression have been developed to infer their biological role. However, such annotations may be unreliable, whereas the evolutionary conservation of gene co-expression among species may form a basis for more confident predictions. The huge amount of expression data (microarrays, SAGE, ESTs) has already allowed functional studies based on conserved co-expression in animals. Up to now, the implementation of analogous tools for plants has been strongly limited probably by the paucity and heterogeneity of data. Here we present ORTom, a tomato-centred EST data-mining approach based on conserved co-expression in the Solanaceae family. ORTom can be used to predict functional relationships among genes and to prioritize candidate genes for targeted studies. The method consists in ranking ESTs co-expressed with a gene of interest according to the level of expression pattern conservation in phylogenetically-related plants (potato, tobacco and pepper) to obtain lists of putative functionally-related genes. The lists are then analyzed for Gene Ontology keyword enrichment. The web server ORTom has been implemented to make the results publicly-available and searchable. Few biological examples on how the tool can be used are presented.