Interpreting Gene Expression Data by Searching for Enriched Gene Sets

Abstract. This paper presents a novel method integrating gene-gene interaction information and Gene Ontology for the construction of new gene sets that are potentially enriched. Enrichment of a gene set is determined by Gene Set Enrichment Analysis, which is a microarray data analysis method that uses ranks of the genes, according to their differentially expression values, to identify significant biological changes in microarray data sets. The experimental results show that the introduced method improves over existing methods, i.e. that it is capable to find new descriptions of the biology governing the experiments, not detectable by the traditional methods of evaluating the enrichment of predefined gene sets, defined by a single GO term.