GeneTrail


    Abstract

    We present a comprehensive and efficient gene set analysis tool, called GeneTrail that offers a rich functionality and is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories. GeneTrail covers a wide variety of biological categories and pathways, among others KEGG, TRANSPATH, TRANSFAC, and GO. Our web server provides two common statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes. Besides other newly developed features, GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the p-value computation of GSEA methods considerably.



    News

    • New analyses/updates/organisms available

    • We now provide the following additional analyses:
      • Wilcoxon-Mann-Whitney test for the distribution of SNPs (from NCBI dbSNP) and Homologues (from NCBI Homologene) in test versus reference set
      • ORA/GSEA for Pfam and Cath protein domains
      • ORA/GSEA for miRNA target genes (from Sanger miRBase)
      • ORA/GSEA for OMIM categories
      Furthermore, we added support for standard file formats for gene sets (.gmt,.gmx) which can be used as input for our self-defined category analysis.

    • GeneTrailExpress paper published

    • The official GeneTrailExpress paper was published in the BMC Bioinformatics journal:

      Keller, A., Backes, C., Al-Awadhi, M., Gerasch, A., Kuentzer, J., Kohlbacher, O., Kaufmann, M., and Lenhof, H.P. GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics 2008, 9:552
      GeneTrailExpress provides comprehensive normalization and scoring functions for pre-processing microarray data. The processed data is directly passed to GeneTrail for statistical evaluation in an extensive gene set analysis.






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