GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining

Statisticalandclusteringanalysesofgeneexpression results from high-density microarray experiments produce lists of hundreds of genes regulated differ-entially, or with particular expression profiles, in the conditions under study. Independent of the micro-array platforms and analysis methods used, these lists must be biologically interpreted to gain a better knowledge of the patho-physiological phenomena involved. To this end, numerous biological annota-tions are available within heterogeneous and widely distributed databases. Although several tools have been developed for annotating lists of genes, most of them do not give methods for evaluating the rele-vance of the annotations provided, or for estimating the functional bias introduced by the gene set on the array used to identify the gene list considered.We developedGenomeFunctional INtegratedDiscoverer (GFINDer), a web server able to automatically provide large-scale lists of user-classified genes with functional profiles biologically characterizing the different gene classes in the list. GFINDer auto-matically retrieves annotations of several functional categories from different sources, identifies the cate-gories enriched ineachclassof auser-classifiedgene list and calculates statistical significance values fo