GeneTrailExpress: a Web-based Pipeline for the Statistical Evaluation of Microarray Experiments

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2008 Dec 23

PMID 19099609

Citations 47

Authors

Andreas Keller

Christina Backes

Maher Al-Awadhi

Andreas Gerasch

Jan Kuntzer

Oliver Kohlbacher

Michael Kaufmann

Hans-Peter Lenhof

Affiliations

Soon will be listed here.

Abstract

Background: High-throughput methods that allow for measuring the expression of thousands of genes or proteins simultaneously have opened new avenues for studying biochemical processes. While the noisiness of the data necessitates an extensive pre-processing of the raw data, the high dimensionality requires effective statistical analysis methods that facilitate the identification of crucial biological features and relations. For these reasons, the evaluation and interpretation of expression data is a complex, labor-intensive multi-step process. While a variety of tools for normalizing, analysing, or visualizing expression profiles has been developed in the last years, most of these tools offer only functionality for accomplishing certain steps of the evaluation pipeline.

Results: Here, we present a web-based toolbox that provides rich functionality for all steps of the evaluation pipeline. Our tool GeneTrailExpress offers besides standard normalization procedures powerful statistical analysis methods for studying a large variety of biological categories and pathways. Furthermore, an integrated graph visualization tool, BiNA, enables the user to draw the relevant biological pathways applying cutting-edge graph-layout algorithms.

Conclusion: Our gene expression toolbox with its interactive visualization of the pathways and the expression values projected onto the nodes will simplify the analysis and interpretation of biochemical pathways considerably.

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References

Keller A, Backes C, Lenhof H . Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics. 2007; 8:290. PMC: 1994690. DOI: 10.1186/1471-2105-8-290. View

Al-Shahrour F, Minguez P, Vaquerizas J, Conde L, Dopazo J . BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 2005; 33(Web Server issue):W460-4. PMC: 1160217. DOI: 10.1093/nar/gki456. View

Nam D, Kim S . Gene-set approach for expression pattern analysis. Brief Bioinform. 2008; 9(3):189-97. DOI: 10.1093/bib/bbn001. View

Vicentini R, Menossi M . Pipeline for macro- and microarray analyses. Braz J Med Biol Res. 2007; 40(5):615-9. DOI: 10.1590/s0100-879x2007000500003. View

Kuntzer J, Backes C, Blum T, Gerasch A, Kaufmann M, Kohlbacher O . BNDB - the Biochemical Network Database. BMC Bioinformatics. 2007; 8:367. PMC: 2092437. DOI: 10.1186/1471-2105-8-367. View

Liu C, Lin C, Chen W, Chen H, Chang P, Chen J . CRSD: a comprehensive web server for composite regulatory signature discovery. Nucleic Acids Res. 2006; 34(Web Server issue):W571-7. PMC: 1538777. DOI: 10.1093/nar/gkl279. View

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View

Maere S, Heymans K, Kuiper M . BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005; 21(16):3448-9. DOI: 10.1093/bioinformatics/bti551. View

Lee H, Braynen W, Keshav K, Pavlidis P . ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinformatics. 2005; 6:269. PMC: 1310606. DOI: 10.1186/1471-2105-6-269. View

10.

Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov J . GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics. 2007; 23(23):3251-3. DOI: 10.1093/bioinformatics/btm369. View

11.

Krull M, Pistor S, Voss N, Kel A, Reuter I, Kronenberg D . TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 2005; 34(Database issue):D546-51. PMC: 1347469. DOI: 10.1093/nar/gkj107. View

12.

Beissbarth T, Speed T . GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics. 2004; 20(9):1464-5. DOI: 10.1093/bioinformatics/bth088. View

13.

Kanehisa M . The KEGG database. Novartis Found Symp. 2003; 247:91-101; discussion 101-3, 119-28, 244-52. View

14.

Edgar R, Domrachev M, Lash A . Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2001; 30(1):207-10. PMC: 99122. DOI: 10.1093/nar/30.1.207. View

15.

Hu Z, Mellor J, Wu J, DeLisi C . VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics. 2004; 5:17. PMC: 368431. DOI: 10.1186/1471-2105-5-17. View

16.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

17.

Al-Shahrour F, Diaz-Uriarte R, Dopazo J . FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics. 2004; 20(4):578-80. DOI: 10.1093/bioinformatics/btg455. View

18.

Zhang B, Kirov S, Snoddy J . WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005; 33(Web Server issue):W741-8. PMC: 1160236. DOI: 10.1093/nar/gki475. View

19.

Sirava M, Schafer T, Eiglsperger M, Kaufmann M, Kohlbacher O, Bornberg-Bauer E . BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics. 2002; 18 Suppl 2:S219-30. DOI: 10.1093/bioinformatics/18.suppl_2.s219. View

20.

Hokamp K, Roche F, Acab M, Rousseau M, Kuo B, Goode D . ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Res. 2004; 32(Web Server issue):W457-9. PMC: 441584. DOI: 10.1093/nar/gkh446. View