|Title||Formulating and testing hypotheses in functional genomics.|
|Publication Type||Journal Article|
|Year of Publication||2009|
|Journal||Artif Intell Med|
|Date Published||2009 Feb-Mar|
|Keywords||Biological Evolution; Computational Biology; Genomics; Genotype; Models, Theoretical|
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.METHODS AND 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.
|Alternate Journal||Artif Intell Med|