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PMID: 17526521 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

GeneTrail--advanced gene set enrichment analysis.

Nucleic acids research ·Vol. 35 ·No. Web Server issue ·2007-07-00 ·Pages W186-92

Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Müller R, Meese E, Lenhof HP

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.

MeSH Terms
Animals Computational Biology/methods Database Management Systems Databases, Genetic Gene Expression Regulation Genes, Fungal Genome Genomics Humans Internet Models, Genetic Models, Statistical Programming Languages Proteomics Software User-Computer Interface
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Backes Christina
Center for Bioinformatics, Saarland University, Building E1.1, 66041 Saarbrücken, Germany. cbackes@bioinf.uni-sb.de
Keller Andreas
Kuentzer Jan
Kneissl Benny
Comtesse Nicole
Elnakady Yasser A
Müller Rolf
Meese Eckart
Lenhof Hans-Peter
References (21)
21 references, click to expand
  1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  2. CRSD: a comprehensive web server for composite regulatory signature discovery.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W571-7 PMID: 16845073
  3. A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer.
    Cell. 2003 Aug 8;114(3):323-34 PMID: 12914697
  4. Development of human protein reference database as an initial platform for approaching systems biology in humans.
    Genome Res. 2003 Oct;13(10):2363-71 PMID: 14525934
  5. The Database of Interacting Proteins: 2004 update.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D449-51 PMID: 14681454
  6. IntAct: an open source molecular interaction database.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D452-5 PMID: 14681455
  7. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
    Bioinformatics. 2004 Mar 1;20(4):578-80 PMID: 14990455
  8. GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
    Bioinformatics. 2004 Jun 12;20(9):1464-5 PMID: 14962934
  9. Predicting coiled coils from protein sequences.
    Science. 1991 May 24;252(5009):1162-4 PMID: 2031185
  10. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4 PMID: 15608248
  11. Comparing functional annotation analyses with Catmap.
    BMC Bioinformatics. 2004 Dec 9;5:193 PMID: 15588298
  12. GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W208-13 PMID: 15980455
  13. BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W460-4 PMID: 15980512
  14. WebGestalt: an integrated system for exploring gene sets in various biological contexts.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W741-8 PMID: 15980575
  15. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.
    Bioinformatics. 2005 Aug 15;21(16):3448-9 PMID: 15972284
  16. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50 PMID: 16199517
  17. ErmineJ: tool for functional analysis of gene expression data sets.
    BMC Bioinformatics. 2005;6:269 PMID: 16280084
  18. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10 PMID: 16381825
  19. From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7 PMID: 16381885
  20. TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D546-51 PMID: 16381929
  21. MINT: a Molecular INTeraction database.
    FEBS Lett. 2002 Feb 20;513(1):135-40 PMID: 11911893
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm323
Email
cbackes@bioinf.uni-sb.de
Published
2007-07-00
Epub
2007-00-25
Pages
W186-92
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1933132
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkm323 PMC Full Text View journal details
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