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A GO-based Method for Assessing the Biological Plausibility of Regulatory Hypotheses
University of Skövde, School of Humanities and Informatics.
University of Skövde, School of Humanities and Informatics.
University of Skövde, School of Humanities and Informatics.
2006 (English)In: ICCS 2006: 6th International Conference on Computational Science, 2006, 879-886 p.Conference paper, (Other academic)
Abstract [en]

Many algorithms have been proposed for deriving regulatory networks from microarray gene expression data. The performance of such algorithms is often measured by how well the resulting network can recreate the gene expression data that it was derived from. However, this kind of performance does not necessarily mean that the regulatory hypotheses in the network are biologically plausible. We therefore propose a method for assessing the biological plausibility of regulatory hypotheses using prior knowledge in the form of regulatory pathway databases and Gene Ontology-based annotation of gene products. A set of templates is derived by generalising from known interactions to typical properties of interacting gene product pairs. By searching for matches in this set of templates, the plausibility of regulatory hypotheses can be assessed. We evaluate to what degree the collection of templates can separate true from false positive interactions, and we illustrate the practical use of the method by applying it to an example network reconstruction problem.

Place, publisher, year, edition, pages
2006. 879-886 p.
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 3992
National Category
Engineering and Technology
Research subject
Technology
Identifiers
URN: urn:nbn:se:his:diva-1863DOI: 10.1007/11758525_117ISI: 000238389400117Scopus ID: 2-s2.0-33746655268ISBN: 978-3-540-34381-3 OAI: oai:DiVA.org:his-1863DiVA: diva2:32139
Available from: 2007-09-12 Created: 2007-09-12 Last updated: 2012-12-10Bibliographically approved

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Gamalielsson, JonasNilsson, PatricOlsson, Björn
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CiteExportLink to record
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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
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