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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Posted ContentDOI
bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays
Kevin Wang,Alexander M. Menzies,Alexander M. Menzies,Ines Pires da Silva,James S. Wilmott,Yibing Yan,Matthew Wongchenko,Richard F. Kefford,Richard A. Scolyer,Richard A. Scolyer,Georgina V. Long,Georgina V. Long,Garth Tarr,Samuel Mueller,Jean Yee Hwa Yang +14 more
TL;DR: The proposed bcGST, a bias-corrected Gene Set Test is proposed by introducing bias correction terms in the contingency table needed for calculating the Fisher's Exact Test (FET) by estimating the proportion of genes captured on the array with respect to the genome.
This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon.
Petra Leidinger,Sabine Müller,Jan D. Haas,Klemens Ruprecht,Christoph Jg,Benjamin Meder,Eckart Meese,Andreas Keller +7 more
Book ChapterDOI
Gene Set Analysis: As Applied to Public Health and Biomedical Studies
Shabnam Vatanpour,Irina Dinu +1 more
TL;DR: This chapter presents a variety of methods for analysis of sets of genes and biological pathways and their association with a given outcome of interest.
Journal ArticleDOI
PRO-Simat: Protein network simulation and design tool
Rana Salihoğlu,Mugdha Srivastava,Chunguang Liang,Klaus Schilling,Aladar A. Szalay,Elena Bencurova,Thomas Dandekar +6 more
TL;DR: Prosimat as discussed by the authors is a simulation tool for analyzing protein interaction networks, their dynamic change and pathway engineering, and provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome.
Journal ArticleDOI
Visuelle Analytik biologischer Daten
Kay Nieselt,Michael Kaufmann,Andreas Gerasch,Hans-Peter Lenhof,Marcel Spehr,Stefan Hesse,Stefan Gumhold +6 more
TL;DR: Die visuelle Analytik biologischer Daten hat erst vor kurzem auf den Information-Visualizationund Visual-Analytics-Konferenzen Beachtung gefunden, das Ziel, die komplexen experimentellen Daten in Wissen umzusetzen.
References
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Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
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Nonparametric Statistical Methods
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