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  PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

Usadel, B., Nagel, A., Steinhauser, D., Gibon, Y., Blaesing, O. E., Redestig, H., et al. (2006). PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics, 7, 535. doi:10.1186/1471-2105-7-535.

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 Creators:
Usadel, B.1, Author              
Nagel, A.2, Author              
Steinhauser, D.3, 4, Author              
Gibon, Y.1, Author              
Blaesing, O. E.5, Author
Redestig, H.6, Author              
Sreenivasulu, N.5, Author
Krall, L.3, Author              
Hannah, M. A.3, Author              
Poree, F.5, Author
Fernie, A. R.7, Author              
Stitt, M.1, Author              
Affiliations:
1System Regulation, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753327              
2BioinformaticsCIG, Infrastructure Groups and Service Units, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753303              
3Small Molecules, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753340              
4Systems Metabolomics, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, Am Mühlenberg 1, 14476 Potsdam-Golm, DE, ou_1797285              
5External Organizations, ou_persistent22              
6BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
7Central Metabolism, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753339              

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Free keywords: Database Management Systems Databases, Genetic *Gene Expression Profiling *Oligonucleotide Array Sequence Analysis *Software/trends *User-Computer Interface
 Abstract: BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. RESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/. CONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments.

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Language(s): eng - English
 Dates: 2006-12-182006
 Publication Status: Published in print
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Title: BMC Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 7 Sequence Number: - Start / End Page: 535 Identifier: -