Using Bayesian networks to analyze expression data

N. Friedman*, M. Linial, I. Nachman, D. Pe'er

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2398 Scopus citations

Abstract

DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a 'snapshot' of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998).

Original languageAmerican English
Pages (from-to)601-620
Number of pages20
JournalJournal of Computational Biology
Volume7
Issue number3-4
DOIs
StatePublished - 2000

Keywords

  • Bayesian methods
  • Gene expression
  • Microarrays

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