The multi-reference contrast method: Facilitating set enrichment analysis.

FRESNO, CRISTOBAL; LLERA, ANDREA SABINA; GIROTTI, MARÍA ROMINA; VALACCO, MARIA P; LOPEZ DEL OLMO, JUAN ANTONIO; PODHAJCER, OSVALDO LUIS; BALZARINI, MÓNICA; PRADA, FEDERICO; FERNÁNDEZ, ELMER ANDRÉS

COMPUTERS IN BIOLOGY AND MEDICINE

PERGAMON-ELSEVIER SCIENCE LTD

Año: 2012 p. 1 - 6

0010-4825

Set 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.