ExprEssence: revealing the essence of differential experimental data in the context of an interaction/regulation net-work

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ExprEssence : revealing the essence of differential experimental data in the context of an interaction/regulation net-work

Warsow, Gregor (author): Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany; Institute for Anatomy and Cell Biology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany; Institute for Anatomy and Cell Biology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany

Greber, Boris (author): Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany

Falk, Steffi S I (author): Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany

Harder, Clemens (author): Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany

Siatkowski, Marcin (author): Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany; DZNE, German Center for Neurodegenerative Disorders, Rostock, Germany

Schordan, Sandra (author): Institute for Anatomy and Cell Biology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany

Som, Anup (author): Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany

Endlich, Nicole (author): Institute for Anatomy and Cell Biology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany

Schöler, Hans (author): Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Medical Faculty, University of Münster, Münster, Germany

Repsilber, Dirk, 1971- (author): Research Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany

Endlich, Karlhans (author): Institute for Anatomy and Cell Biology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany

Fuellen, Georg (author): Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany

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2010-11-30
2010
English.
In: BMC Systems Biology. - London, UK : BioMed Central (BMC). - 1752-0509. ; 4, s. 164-

Related links:: https://doi.org/10.1...; show more...; https://bmcsystbiol....; https://urn.kb.se/re...; https://doi.org/10.1...; show less...

Journal article (peer-reviewed)

Abstract Subject headings

Background: Experimentalists are overwhelmed by high-throughput data and there is an urgent need to condense information into simple hypotheses. For example, large amounts of microarray and deep sequencing data are becoming available, describing a variety of experimental conditions such as gene knockout and knockdown, the effect of interventions, and the differences between tissues and cell lines.Results: To address this challenge, we developed a method, implemented as a Cytoscape plugin called ExprEssence. As input we take a network of interaction, stimulation and/or inhibition links between genes/proteins, and differential data, such as gene expression data, tracking an intervention or development in time. We condense the network, highlighting those links across which the largest changes can be observed. Highlighting is based on a simple formula inspired by the law of mass action. We can interactively modify the threshold for highlighting and instantaneously visualize results. We applied ExprEssence to three scenarios describing kidney podocyte biology, pluripotency and ageing: 1) We identify putative processes involved in podocyte (de-)differentiation and validate one prediction experimentally. 2) We predict and validate the expression level of a transcription factor involved in pluripotency. 3) Finally, we generate plausible hypotheses on the role of apoptosis, cell cycle deregulation and DNA repair in ageing data obtained from the hippocampus.Conclusion: Reducing the size of gene/protein networks to the few links affected by large changes allows to screen for putative mechanistic relationships among the genes/proteins that are involved in adaptation to different experimental conditions, yielding important hypotheses, insights and suggestions for new experiments. We note that we do not focus on the identification of 'active subnetworks'. Instead we focus on the identification of single links (which may or may not form subnetworks), and these single links are much easier to validate experimentally than submodules. ExprEssence is available at http://sourceforge.net/projects/expressence/.

Subject headings

NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)

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By the author/editor: Warsow, Gregor; Greber, Boris; Falk, Steffi S I; Harder, Clemens; Siatkowski, Marc ...; Schordan, Sandra; show more...; Som, Anup; Endlich, Nicole; Schöler, Hans; Repsilber, Dirk, ...; Endlich, Karlhan ...; Fuellen, Georg; show less...

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

Articles in the publication: BMC Systems Biol ...

By the university: Örebro University

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