Max-Planck-Institut für Informatik
max planck institut
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The analysis of gene expression data is an important tool for understanding mechanisms of living systems. Microarray experiments provide large amounts of data, but it is difficult to understand biological processes or molecular functions from such data alone.

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. topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Adrian Alexa