NuGO contributions to GenePattern

P. J. De Groot, Caroline Reiff, Claus-Dieter Mayer, M. Mueller

Research output: Contribution to journalEditorialpeer-review

26 Citations (Scopus)


NuGO, the European Nutrigenomics Organization, utilizes 31 powerful computers for, e.g., data storage and analysis. These so-called black boxes (NBXses) are located at the sites of different partners. NuGO decided to use GenePattern as the preferred genomic analysis tool on each NBX. To handle the custom made Affymetrix NuGO arrays, new NuGO modules are added to GenePattern. These NuGO modules execute the latest Bioconductor version ensuring up-to-date annotations and access to the latest scientific developments. The following GenePattern modules are provided by NuGO: NuGOArrayQualityAnalysis for comprehensive quality control, NuGOExpressionFileCreator for import and normalization of data, LimmaAnalysis for identification of differentially expressed genes, TopGoAnalysis for calculation of GO enrichment, and GetResultForGo for retrieval of information on genes associated with specific GO terms. All together, these NuGO modules allow comprehensive, up-to-date, and user friendly analysis of Affymetrix data. A special feature of the NuGO modules is that for analysis they allow the use of either the standard Affymetrix or the MBNI custom CDF-files, which remap probes based on current knowledge. In both cases a .chip-file is created to enable GSEA analysis. The NuGO GenePattern installations are distributed as binary Ubuntu (.deb) packages via the NuGO repository.

Original languageEnglish
Pages (from-to)143-146
Number of pages4
JournalGenes & Nutrition
Issue number3-4
Publication statusPublished - Dec 2008


  • GenePattern
  • GetResultsForGo
  • LimmaAnalysis
  • NuGOArrayQualityAnalysis
  • NuGOExpressionFileCreator
  • TopGoAnalysis


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