Formulating and testing hypotheses in functional genomics

TitleFormulating and testing hypotheses in functional genomics
Publication TypeJournal Article
Year of Publication2009
AuthorsDopazo, J
JournalArtif Intell Med
Volume45
Pagination97-107
Keywordsbabelomics; gene set analysis
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. 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.

Notes

Dopazo, Joaquin Research Support, Non-U.S. Gov’t Netherlands Artificial intelligence in medicine Artif Intell Med. 2009 Feb-Mar;45(2-3):97-107. Epub 2008 Sep 11.

URLhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18789659