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
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Journal ArticleDOI
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes
TL;DR: A new method for gene set analysis that is based on principal component analysis (PCA) of genes expression values in the gene set, thus called the Supervised PCA model, and it is shown the proposed method compares favorably to currently available gene setAnalysis methods using simulated and real microarray data.
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Parallel Selection Mapping Using Artificially Selected Mice Reveals Body Weight Control Loci
Yingguang Frank Chan,Felicity C. Jones,Ellen McConnell,Jarosław Bryk,Lutz Bünger,Diethard Tautz +5 more
TL;DR: The data suggest that parallel selection on complex traits may evoke parallel responses at many genes involved in diverse but relevant pathways, possibly through evolutionary conserved functional pathways.
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miRNAs can be generally associated with human pathologies as exemplified for miR-144*
Andreas Keller,Petra Leidinger,Britta Vogel,Christina Backes,Abdou ElSharawy,Valentina Galata,Sabine C. Mueller,Sabine Marquart,Michael G. Schrauder,Reiner Strick,Andrea S. Bauer,J�rg Wischhusen,Markus Beier,Jochen Kohlhaas,Hugo A. Katus,J�rg D. Hoheisel,Andre Franke,Benjamin Meder,Eckart Meese +18 more
TL;DR: This study on 1,368 patients including 1,049 genome-wide miRNA profiles and 319 qRT-PCR validations further underscores the high potential of specific blood-borne miRNA patterns as molecular biomarkers.
Journal ArticleDOI
Toward a gold standard for benchmarking gene set enrichment analysis.
Ludwig Geistlinger,Gergely Csaba,Mara Santarelli,Marcel Ramos,Lucas Schiffer,Nitesh Turaga,Charity W. Law,Sean Davis,Vincent J. Carey,Martin Morgan,Ralf Zimmer,Levi Waldron +11 more
TL;DR: An extensible framework for reproducible benchmarking of enrichment methods based on defined criteria for applicability, gene set prioritization and detection of relevant processes is developed.
Journal ArticleDOI
Gene expression profiling in vastus lateralis muscle during an acute exacerbation of COPD.
Tim Crul,Dries Testelmans,Martijn A. Spruit,Thierry Troosters,Rik Gosselink,Ineke Geeraerts,Marc Decramer,Ghislaine Gayan-Ramirez +7 more
TL;DR: The present study suggests that multiple pathways leading to muscle atrophy and mitochondrial dysfunction are altered in the muscle during an acute exacerbation and strategies limiting the loss of muscle function need to be developed.
References
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