topGO (topology-based Gene Ontology scoring) is a software package for calculating the significance of biological terms from gene expression data. It implements various standard and advanced new algorithms for determining the relevance of Gene Ontology groups from microarrays. A specific feature of the advanced algorithms is the exploitation of the hierarchical graph structure of the GO annotation for coping with the large number of GO groups. Often, related biological terms are scored with a similar statistical significance. Dependencies between GO terms can be de-correlated by accounting for the neighborhood of a GO node when calculating its significance. The new algorithms better detect significant GO terms from gene expression data.
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Alexa, A.; Rahnenführer, J.; Lengauer, T.,
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure.
Bioinformatics 2006, 22 (13), 1600-7.