Comparing background reference results in proteomics-based Gene Ontology analysis

CRISTÓBAL FRESNO; ANDREA S LLERA; MARÍA ROMINA GIROTTI; MARÍA FLORENCIA STRAMINSKY; MARÍA PÍA VALACCO; MONICA BALZARINI; FEDERICO PRADA; ELMER A FERNÁNDEZ; PODHAJCER OSVALDO

Congreso; 2do Congreso Argentino de Bioinformática y Biología Computacional; 2011

In genomics or proteomics experiments there is often the need to identify biological processes or functions that are relevantly affected by a stimulus. Set enrichment analysis (SEA) is a bioinformatics tool that intends to give an answer to this need. SEA evaluates the proportion of differentially expressed genes/proteins against a background reference (BR) in order to identify enriched biological categories/terms [1]. It is acknowledged that different BRs may produce different results [2]. This fact led us to think that, depending on the used BR, the researcher might miss biologically relevant terms. Here we contrast the results obtained with two references for a proteomic study in which not all possible proteins could be seen due to biological and/or experimental constrains.