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A Gene Ontology 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.
2005 (English)Report (Other academic)
Abstract [en]

Many algorithms that derive gene regulatory networks from microarray gene expression data have been proposed in the literature. The performance of such an algorithm is often measured by how well a genetic network can recreate the gene expression data that the network 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 Gene Ontology based method for assessing the biological plausibility of regulatory hypotheses at the gene product level using prior biological knowledge in the form of Gene Ontology annotation of gene products and regulatory pathway databases. Templates are designed to encode general knowledge, derived by generalizing from known interactions to typical properties of interacting gene product pairs. By matching regulatory hypotheses to templates, the plausible hypotheses can be separated from inplausible ones. In a cross-validation test we verify that the templates reliably identify interactions which have not been used in the template creation process, thereby confirming the generality of the approach. The method also proves useful when applied to an example network reconstruction problem, where a Bayesian approach is used to create hypothetical relations which are evaluated for biological plausibility. The cell cycle pathway and the MAPK signaling pathway for S. cerevisiae and H. sapiens are used in the experiments.

Place, publisher, year, edition, pages
Skövde: Institutionen för kommunikation och information , 2005. , 10 p.
Series
IKI Technical Reports, HS-IKI-TR-05-004
National Category
Information Science
Identifiers
URN: urn:nbn:se:his:diva-1261OAI: oai:DiVA.org:his-1261DiVA: diva2:2397
Available from: 2008-06-17 Created: 2008-06-17 Last updated: 2012-12-17Bibliographically approved

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Gamalielsson, JonasOlsson, BjörnNilsson, Patric
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CiteExportLink to record
Permanent link

Direct link
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
  • rtf