Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks

Seiya Imoto, Tomoyuki Higuchi, Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano

Research output: Contribution to journalArticlepeer-review

79 Citations (Scopus)

Abstract

We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including protein-protein interactions, protein-DNA interactions, binding site information, existing literature and so on. Microarray data do not contain enough information for constructing gene networks accurately in many cases. Our method adds biological knowledge to the estimation method of gene networks under a Bayesian statistical framework, and also controls the trade-off between microarray information and biological knowledge automatically. We conduct Monte Carlo simulations to show the effectiveness of the proposed method. We analyze Saccharomyces cerevisiae gene expression data as an application.

Original languageEnglish
Pages (from-to)77-98
Number of pages22
JournalJournal of bioinformatics and computational biology
Volume2
Issue number1
DOIs
Publication statusPublished - Mar 2004

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

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