Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists

Motivation: The ontological analysis of the gene lists obtained from DNA microarray experiments constitutes an important step in understanding the underlying biology of the analyzed system. Over the last years, many other high-throughput techniques emerged, covering now basically all omics fields. However, for some of these techniques the generally used functional ontologies might not be sufficient to describe the biological system represented by the derived gene lists. For a more complete and correct interpretation of these experiments, it is important to extend substantially the number of annotations, adapting the ontological analysis to the new emerging techniques. Results: We developed Annotation-Modules, which offers an improvement over the current tools in two critical aspects. First, the underlying annotation database implements features from many different fields like gene regulation and expression, sequence properties, evolution and conservation, genomic localization and functional categoriesresulting in about 60 different annotation features. Second, it examines not only single annotations but also all the combinations, which is important to gain insight into the interplay of different mechanisms in the analyzed biological system.