“Is there strength in numbers? Looking the best background reference in ontology analysis”

CRISTÓBAL FRESNO; ANDREA S LLERA; GIROTTI, MARÍA ROMINA; MARÍA PÍA VALACCO; LOPEZ DEL OLMO, JUAN ANTONIO; OSVALDO L PODHAJCER; BALZARINI, MÓNICA; FEDERICO PRADA; FERNÁNDEZ, ELMER ANDRÉS

Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Congreso; Functional Genomics and Systems Biology Conference 2011; 2011

Wellcome Trust, UK

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.