title: ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato.
abstract: 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.
authors.affiliation: Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Turin, Italy. l.miozzi@ivv.cnr.it
authors.forename: Laura
authors.initials: L
authors.lastname: Miozzi
authors.forename: Paolo
authors.initials: P
authors.lastname: Provero
authors.forename: Gian Paolo
authors.initials: GP
authors.lastname: Accotto
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D057225:Data Mining / Q000379:methods*; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics*; D054884:Host-Pathogen Interactions / Q000235:genetics; D020407:Internet; D018551:Solanum lycopersicum / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012985:Software Design; D013045:Species Specificity
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