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Inferring Genetic Networks from Expression Data with Mutual Information
University of Skövde, Department of Computer Science.
2002 (English)Independent thesis Advanced level (degree of Master (One Year))Student thesis
Abstract [en]

Recent methods to infer genetic networks are based on identifying gene interactions by similarities in expression profiles. These methods are founded on the assumption that interacting genes share higher similarities in their expression profiles than non-interacting genes. In this dissertation this assumption is validated when using mutual information as a similarity measure. Three algorithms that calculate mutual information between expression data are developed: 1) a basic approach implemented with the histogram technique; 2) an extension of the basic approach that takes into consideration time delay between expression profiles; 3) an extension of the basic approach that takes into consideration that genes are regulated in a complex manner by multiple genes. In our experiments we compare the mutual information distributions for profiles of interacting and non-interacting genes. The results show that interacting genes do not share higher mutual information in their expression profiles than non-interacting genes, thus contradicting the basic assumption that similarity measures need to fulfil. This indicates that mutual information is not appropriate as similarity measure, which contradicts earlier proposals.

Place, publisher, year, edition, pages
Skövde: Institutionen för datavetenskap , 2002. , 91 p.
Keyword [en]
Gene Expression, Gene Expression Analysis, Genetic Networks, Gene Regulation, Mutual Information
National Category
Information Science
Identifiers
URN: urn:nbn:se:his:diva-736OAI: oai:DiVA.org:his-736DiVA: diva2:3139
Presentation
(English)
Uppsok
Social and Behavioural Science, Law
Supervisors
Available from: 2008-02-06 Created: 2008-02-06 Last updated: 2009-10-09

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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