title: Formulating and testing hypotheses in functional genomics.
abstract: OBJECTIVE
  The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the results, relating the available genomic information to the hypotheses that originated the experiment.
  
  
  RESULTS
  Initially, this interpretation has been made on a pre-selection of relevant genes, based on the experimental values, followed by the study of the enrichment in some functional properties. Nevertheless, functional enrichment methods, demonstrated to have a flaw: the first step of gene selection was too stringent given that the cooperation among genes was ignored. The assumption that modules of genes related by relevant biological properties (functionality, co-regulation, chromosomal location, etc.) are the real actors of the cell biology lead to the development of new procedures, inspired in systems biology criteria, generically known as gene-set methods. These methods have been successfully used to analyze transcriptomic and large-scale genotyping experiments as well as to test other different genome-scale hypothesis in other fields such as phylogenomics.
authors.affiliation: Department of Bioinformatics, and Functional Genomics Node (INB), Valencia E-46013, Spain. jdopazo@cipf.es
authors.forename: Joaquin
authors.initials: J
authors.lastname: Dopazo
mesh_terms: D005075:Biological Evolution; D019295:Computational Biology; D023281:Genomics; D005838:Genotype; D008962:Models, Theoretical