Handling and interpreting gene groups

Abstract

Systems biologists often have to deal with large gene groups obtained from high-throughput experiments, genome-wide predictions, and literature searches. Handling and functional interpretation of these gene groups is rather challenging. Problems arise from redundancies in databases, where a gene is given several names or identifiers, and from falsely assigned genes in the list. Moreover, genes in gene groups obtained by different methods are often represented by different types of identifiers, or are even genes from other model organisms. Thus, research in systems biology requires software tools that help to handle and interpret gene groups. This chapter will review tools to store and compare gene groups represented by various identifiers. We introduce software that uses Gene Ontology (GO) annotations to infer biological processes associated with the gene groups. Additionally, we review approaches to further analyze gene groups regarding their transcriptional regulation by retrieving and analyzing their putative promoter regions. © 2007 Humana Press Inc.