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
Reads0
Chats0
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
More filters
Journal ArticleDOI
A Possible Mechanism behind Autoimmune Disorders Discovered By Genome-Wide Linkage and Association Analysis in Celiac Disease
Malin Östensson,Caroline Montén,Jonas Bacelis,Audur H. Gudjonsdottir,Svetlana Adamovic,Johan Ek,Henry Ascher,Elisabet Pollak,Henrik Arnell,Lars Browaldh,Daniel Agardh,Jan Wahlström,Staffan Nilsson,Åsa Torinsson-Naluai,Åsa Torinsson-Naluai +14 more
TL;DR: A GWAS including 206 trios from 97 nuclear Swedish and Norwegian families affected with celiac disease and a new genome-wide significant risk locus covering the DUSP10 gene is identified, revealing a new potential biological mechanism that could influence the genesis of Celiac disease, and possibly also other chronic disorders with an inflammatory component.
Journal ArticleDOI
BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma
Daniel Nettersheim,Sina Jostes,Rakesh Sharma,Simon Schneider,Andrea Hofmann,Humberto J. Ferreira,Per Hoffmann,Glen Kristiansen,Manel Esteller,Hubert Schorle +9 more
TL;DR: It is demonstrated that inhibition of BMP signaling is the initial event in reprogramming, resulting in activation of the pluripotency-associated genes and NODAL signaling and it is proposed that reprograming of seminomas to ECs is a multi-step process.
Journal ArticleDOI
Computation of significance scores of unweighted Gene Set Enrichment Analyses
TL;DR: A novel dynamic programming algorithm for calculating exact significance values of unweighted Gene Set Enrichment Analyses is presented, which avoids typical problems of nonparametric permutation tests, as varying findings in different runs caused by the random sampling procedure.
Journal ArticleDOI
AML at older age: age-related gene expression profiles reveal a paradoxical down-regulation of p16INK4A mRNA with prognostic significance.
Hendrik J. M. de Jonge,Eveline S. J. M. de Bont,Peter J. M. Valk,Jan Jacob Schuringa,P. Marcel Kies,Carolien M. Woolthuis,Ruud Delwel,Nic J. G. M. Veeger,Edo Vellenga,Bob Löwenberg,Gerwin Huls +10 more
TL;DR: Multivariate analysis revealed p16(INK4A), besides cytogenetic risk groups, as an independent prognostic parameter for overall survival in older patients.
Journal ArticleDOI
Prioritizing risk pathways
TL;DR: This work proposed an approach to prioritize risk pathways for complex diseases: Prioritizing Risk Pathways fusing SNPs and pathways (PRP), and introduced this approach to five complex diseases and found that these five diseases not only share common risk pathways, but also have their specific risk paths, which is verified by literature retrieval.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
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.
Book
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.
Journal ArticleDOI
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.
Related Papers (5)
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
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more