GeneTrail—advanced gene set enrichment analysis
Christina Backes,Andreas Keller,Jan Kuentzer,Benny Kneissl,Nicole Comtesse,Yasser A. Elnakady,Rolf Müller,Eckart Meese,Hans-Peter Lenhof +8 more
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TLDR
GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the P-value computation of GSEA methods considerably and is freely accessible at http://genetrail.uni-sb.de.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. GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.de.read more
Citations
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Blood-based gene expression signatures in non-small cell lung cancer
Thomas Zander,Andrea Hofmann,Andrea Staratschek-Jox,Sabine Classen,Svenja Debey-Pascher,Daniela Maisel,Sascha Ansén,Moritz Hahn,Marc Beyer,Roman K. Thomas,Birgit S. Gathof,Cornelia Mauch,Karl-Stefan Delank,Walburga Engel-Riedel,H.-Erich Wichmann,Erich Stoelben,Joachim L. Schultze,Juergen Wolf +17 more
TL;DR: The results show that gene expression profiles of whole blood allow for detection of manifest NSCLC, and prompt further development of gene expression–based biomarker tests in peripheral blood for the diagnosis and early detection ofNSCLC.
Journal ArticleDOI
An introduction to effective use of enrichment analysis software.
Hannah Tipney,Lawrence Hunter +1 more
TL;DR: Three classes of enrichment algorithms and their associated software implementations are introduced here and their limitations and caveats are discussed, and direction for tool selection is given.
Journal ArticleDOI
Natalizumab restores aberrant miRNA expression profile in multiple sclerosis and reveals a critical role for miR‐20b
Jens Ingwersen,Til Menge,Britta Wingerath,Derya Kaya,Jonas Graf,Tim Prozorovski,Andreas Keller,Christina Backes,Markus Beier,Matthias Scheffler,Thomas Dehmel,Bernd C. Kieseier,Hans-Peter Hartung,Patrick Küry,Orhan Aktas +14 more
TL;DR: To identify microRNAs regulated by anti‐α4 integrin monoclonal antibody therapy (natalizumab) in the peripheral blood of patients with relapsing‐remitting multiple sclerosis (RR) multiple sclerosis and to confirm their role in experimental settings in vivo.
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The functional genomic studies of curcumin.
TL;DR: Here, a review of the published functional genomic studies of curcumin focusing on cancer finds genes involved in cell signaling, apoptosis, and the control of cell cycle among differentially expressed genes are found.
Journal ArticleDOI
Next-generation sequencing identifies novel microRNAs in peripheral blood of lung cancer patients
Andreas Keller,Andreas Keller,Christina Backes,Petra Leidinger,Nathalie Kefer,Valesca Boisguerin,Catalin Barbacioru,Britta Vogel,Mark Matzas,Hanno Huwer,Hugo A. Katus,Cord F. Stähler,Benjamin Meder,Eckart Meese +13 more
TL;DR: It is demonstrated that deep sequencing of small RNAs bears high potential to quantify miRNAAs in peripheral blood and to identify previously unknown miRNAs serving as biomarker for lung cancer, and developed a bioinformatics pipeline to generate profiles of miRNA markers and to detect novel mi RNAs with diagnostic information.
References
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