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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Dissertation
A Statistical Framework for Incorporating Multi-Omics Technologies for Precision Medicine
TL;DR: This thesis addresses important statistical challenges in precision medicine, the clinical practice to customise treatment plans for individual patients using genetic information by proposing methods, frameworks and procedures that tackle the discovery, translation and implementation of precision medicine through the use of omics data.
Posted ContentDOI
GenFam: A new web application for gene family-based classification and functional enrichment analysis of plant genomes
Renesh Bedre,Renesh Bedre,Renesh Bedre,Renesh Bedre,Renesh Bedre,Renesh Bedre,Kranthi K. Mandadi +6 more
TL;DR: GenFam as mentioned in this paper proposes a robust functional enrichment approach, GenFam, to classify as well as enrich overrepresented gene functions, based on gene family categories, which offers a unique approach to mine valuable, biologically-relevant information, beyond the conventional GO term based enrichment.
Heat shock protein gp96 drives dichotomous lymphocyte responses via dna methylome remodeling and stat1 signaling in antigen presenting cells
TL;DR: A CD91-dependent mechanism through which gp96 controls dichotomous immune responses, relevant to the therapy of cancer and autoimmunity is defined, which hypothesizes that STAT1 activation in responding APCs is necessary for tumor rejection.
Journal ArticleDOI
GeneTrail: A Framework for the Analysis of High-Throughput Profiles.
Nico Gerstner,Tim Kehl,Kerstin Lenhof,Lea Eckhart,Lara Schneider,Daniel Stöckel,Christina Backes,Eckart Meese,Andreas Keller,Hans-Peter Lenhof +9 more
TL;DR: The GeneTrail tool suite as discussed by the authors offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles, and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes.
References
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Yoav Benjamini,Yosef Hochberg +1 more
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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
Myles Hollander,Douglas A. Wolfe +1 more
TL;DR: An ideal text for an upper-level undergraduate or first-year graduate course, Nonparametric Statistical Methods, Second Edition is also an invaluable source for professionals who want to keep abreast of the latest developments within this dynamic branch of modern statistics.
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
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