Fresno, CristóbalLlera, Andrea SGirotti, María RValacco, María PLopez, Juan AntonioPodhajcer, Osvaldo LBalzarini, Mónica GPrada, FedericoFernández, Elmer A2019-05-232019-05-232012-02Comput Biol Med. 2012; 42(2):188-9400104825http://hdl.handle.net/20.500.12105/7672Set enrichment analysis (SEA) is used to identify enriched biological categories/terms within high-throughput differential expression experiments. This is done by evaluating the proportion of differentially expressed genes against a background reference (BR). However, the choice of the "appropriate" BR is a perplexing problem and results will depend on it. Here, a visualization procedure that integrates results from several BRs and a stability analysis of enriched terms is presented as a tool to aid SEA. The multi-reference contrast method (MRCM) combines results from multiple BRs in a unique picture. The application of the proposed method was illustrated in one proteomic and three microarray experiments. The MRCM facilitates the exploration task involved in ontology analysis on proteomic/genomic experiments, where consensus terms were found to validate main experimental hypothesis. The use of more than one reference may provide new biological insights. The tool automatically highlights non-consensus terms assisting SEA.engAMhttp://creativecommons.org/licenses/by-nc-nd/4.0/AnimalsCluster AnalysisData MiningElectrophoresis, Gel, Two-DimensionalGene Expression ProfilingGenomicsHumansMiceModels, TheoreticalOligonucleotide Array Sequence AnalysisProteomicsDatabases, GeneticTerminology as TopicAttribution-NonCommercial-NoDerivatives 4.0 Internacional22226646422188-9410.1016/j.compbiomed.2011.11.0071879-0534Computers in biology and medicineopen access