Modelling gene functional linkages using yeast microarray data

Tie Wang, Guoliang Xue, Jeffrey W. Touchman

Research output: Contribution to journalArticle

Abstract

Understanding how genes are functionally related requires efficient algorithms to model networks from expression data. We report a heuristic search algorithm called Two-Level Simulated Annealing (TLSA) that is more likely to find me global optimal network structure compared to conventional simulated annealing and other searching schemes. We have applied this method to search for a global optimised network structure from a synthetic data set and an expression data set of S. cerevisiae mutants. We have achieved better precision and recall compared to other searching algorithms and are able to map relationships more accurately among functionally-linked genes.

Original languageEnglish (US)
Pages (from-to)170-186
Number of pages17
JournalInternational Journal of Bioinformatics Research and Applications
Volume3
Issue number2
DOIs
Publication statusPublished - 2007

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Keywords

  • ANOVA
  • Bioinformatics
  • Correlation
  • Differential expression analysis
  • DNA microarrays
  • Replication
  • Sources of variation

ASJC Scopus subject areas

  • Health Informatics
  • Health Information Management
  • Biomedical Engineering
  • Clinical Biochemistry

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