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Authors: Nils Blüthgen Szymon M Kielbasa Dieter Beule
Publish Date: 2007
Volume: , Issue: , Pages: 69-84
Abstract
Systems biologists often have to deal with large gene groups obtained from highthroughput experiments genomewide 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 groupsThis 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
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