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Most methods for the interpretation of gene expression profiling experiments rely on the categorization of genes, as provided by the Gene Ontology (GO) and pathway databases. Due to the manual curation process, such databases are never up-to-date and tend to be limited in focus and coverage. Automated literature mining tools provide an attractive, alternative approach. We review how they can be employed for the interpretation of gene expression profiling experiments. We illustrate that their comprehensive scope aids the interpretation of data from domains poorly covered by GO or alternative databases, and allows for the linking of gene expression with diseases, drugs, tissues and other types of concepts. A framework for proper statistical evaluation of the associations between gene expression values and literature concepts was lacking and is now implemented in a weighted extension of global test. The weights are the literature association scores and reflect the importance of a gene for the concept of interest. In a direct comparison with classical GO-based gene sets, we show that use of literature-based associations results in the identification of much more specific GO categories. We demonstrate the possibilities for linking of gene expression data to patient survival in breast cancer and the action and metabolism of drugs. Coupling with online literature mining tools ensures transparency and allows further study of the identified associations. Literature mining tools are therefore powerful additions to the toolbox for the interpretation of high-throughput genomics data.

Literature-aided interpretation of gene expression data with the weighted global test