The Multi-Reference Contrast Method: facilitating set enrichment analysis

CRISTÓBAL FRESNO; ANDREA S LLERA; MARÍA R GIROTTI; MARÍA PÍA VALACCO; JUAN A LÓPEZ; OSVALDO L PODHAJCER; MÓNICA G BALZARINI; FEDERICO PRADA; ELMER A FERNÁNDEZ

COMPUTERS IN BIOLOGY AND MEDICINE

PERGAMON-ELSEVIER SCIENCE LTD

Lugar: BethesdaArborvitae, 8700 Garfield St, Bethesda, MD 20817, USA ; Año: 2012 vol. 42 p. 188 - 194

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.