An open graph visualization system and its applications to software engineering
Software—Practice & Experience - Special issue on discrete algorithm engineering
Compositional mining of multirelational biological datasets
ACM Transactions on Knowledge Discovery from Data (TKDD)
SEGS: Search for enriched gene sets in microarray data
Journal of Biomedical Informatics
Discovering Local Patterns of Co-evolution
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
EURASIP Journal on Bioinformatics and Systems Biology
Validating gene clusterings by selecting informative gene ontology terms with mutual information
BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
TreeHugger: A New Test for Enrichment of Gene Ontology Terms
INFORMS Journal on Computing
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We propose an improved statistic for detecting over-represented Gene Ontology (GO) annotations in gene sets. While the current methods treats each term independently and hence ignores the structure of the GO hierarchy, our approach takes parent-child relationships into account. Over-representation of a term is measured with respect to the presence of its parental terms in the set. This resolves the problem that the standard approach tends to falsely detect an over-representation of more specific terms below terms known to be over-represented. To show this, we have generated gene sets in which single terms are artificially over-represented and compared the receiver operator characteristics of the two approaches on these sets. A comparison on a biological dataset further supports our method. Our approach comes at no additional computational complexity when compared to the standard approach. An implementation is available within the framework of the freely available Ontologizer application.