Mining Gene Ontology Data with AGENDA

Abstract

The Gene Ontology (GO) initiative is a collaborative effort that uses controlled vocabularies for annotating genetic information. We here present AGENDA (Application for mining Gene Ontology Data), a novel web-based tool for accessing the GO database. AGENDA allows the user to simultaneously retrieve and compare gene lists linked to different GO terms in diverse species using batch queries, facilitating comparative approaches to genetic information. The web-based application offers diverse search options and allows the user to bookmark, visualize, and download the results. AGENDA is an open source web-based application that is freely available for non-commercial use at the project homepage. URL: http://sourceforge.net/projects/bioagenda.

Keywords: Gene Ontology; complex query; controlled vocabulary; data mining; gene annotation.

Figure 1

Screenshot of the “GO Slimmer” option in AGENDA. The screenshot displays the cellular localizations of human genes that are implicated in apoptosis. Notes: 1771 genes are identified that are associated with apoptosis (GO:0006915). 235 of the respective gene products localize, for example, to the mitochondrion (GO:0005739), 591 to the plasma membrane (GO:0005886), and 938 to the nucleus (GO:0005634).