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Nucleic Acids Research Advance Access published online on May 25, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm323
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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GeneTrail—advanced gene set enrichment analysis

Christina Backes1,*, Andreas Keller1, Jan Kuentzer1, Benny Kneissl1, Nicole Comtesse2, Yasser A. Elnakady3, Rolf Müller3, Eckart Meese2 and Hans-Peter Lenhof1

1Center for Bioinformatics, Saarland University, Building E1.1, 66041 Saarbrücken, 2Department of Human Genetics, Medical School, Building 60, 66421 Homburg/Saar and 3Department of Pharmaceutical Biotechnology, Saarland University, Building A4.1, 66041 Saarbrücken, Germany

*To whom correspondence should be addressed. Tel: +49-681-302-68608; Fax: +49-681-302-64719; Email: cbackes{at}bioinf.uni-sb.de

Received January 31, 2007. Revised April 6, 2007. Accepted April 17, 2007.

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. GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de

The authors wish to be known that, in their opinion, this first two authors should be regarded as joint First Authors.


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