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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Toward the blood-borne miRNome of human diseases
Andreas Keller,Petra Leidinger,Andrea S. Bauer,Abdou ElSharawy,Jan Haas,Christina Backes,Anke Wendschlag,Nathalia Giese,Christine Tjaden,Katja Ott,Jens Werner,Thilo Hackert,Klemens Ruprecht,Hanno Huwer,Junko Huebers,Gunnar Jacobs,Philip Rosenstiel,Henrik Dommisch,Arne S. Schaefer,Joachim Müller-Quernheim,Bernd Wullich,Bastian Keck,Norbert Graf,Joerg Reichrath,Britta Vogel,Almut Nebel,Sven Uwe Jager,Peer F Staehler,Ioannis Amarantos,Valesca Boisguerin,Cord F Staehler,Markus Beier,Matthias Scheffler,Markus W. Büchler,J Wischhusen,Sebastian F M Haeusler,Johannes Dietl,Sylvia Hofmann,Hans-Peter Lenhof,Stefan Schreiber,Hugo A. Katus,Wolfgang Rottbauer,Benjamin Meder,Joerg Hoheisel,Andre Franke,Eckart Meese +45 more
TL;DR: In a multicenter study, the expression profiles of 863 microRNAs were determined by array analysis of 454 blood samples from human individuals with different cancers or noncancer diseases, and this 'miRNome' was validated by quantitative real-time PCR.
Journal ArticleDOI
EnrichNet: network-based gene set enrichment analysis
TL;DR: An integrative analysis approach and web-application that combines a novel graph-based statistic with an interactive sub-network visualization to accomplish two complementary goals: improving the prioritization of putative functional gene/protein set associations by exploiting information from molecular interaction networks and tissue-specific gene expression data and enabling a direct biological interpretation of the results.
Journal ArticleDOI
Gene-set approach for expression pattern analysis
Dougu Nam,Seon-Young Kim +1 more
TL;DR: Recently developed gene set analysis methods evaluate differential expression patterns of gene groups instead of those of individual genes, which has been quite successful in deriving new information from expression data.
Journal ArticleDOI
An integer linear programming approach for finding deregulated subgraphs in regulatory networks
Christina Backes,Alexander Rurainski,Gunnar W. Klau,Oliver Müller,Daniel Stöckel,Andreas Gerasch,Jan Küntzer,Daniela Maisel,Nicole Ludwig,Matthias Hein,Andreas Keller,Helmut Burtscher,Michael Kaufmann,Eckart Meese,Hans-Peter Lenhof +14 more
TL;DR: The results suggest that oxidative stress plays an important role in epithelial cells of BRCA1 mutation carriers and that the activation of stress proteins may result in avoidance of apoptosis leading to an increased overall survival of cells with genetic alterations.
Journal ArticleDOI
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures
Qiaonan Duan,Corey Flynn,Mario Niepel,Marc Hafner,Jeremy L. Muhlich,Nicolas F. Fernandez,Andrew D. Rouillard,Christopher M. Tan,Edward Y. Chen,Todd R. Golub,Peter K. Sorger,Aravind Subramanian,Avi Ma'ayan +12 more
TL;DR: LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data.
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