Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection

Yoshinori Tamada, Sun Yong Kim, Hideo Bannai, Seiya Imoto, Kosuke Tashiro, Satoru Kuhara, Satoru Miyano

Research output: Contribution to journalArticle

137 Citations (Scopus)

Abstract

We present a statistical method for estimating gene networks and detecting promoter elements simultaneously. When estimating a network from gene expression data alone, a common problem is that the number of microarrays is limited compared to the number of variables in the network model, making accurate estimation a difficult task. Our method overcomes this problem by integrating the microarray gene expression data and the DNA sequence information into a Bayesian network model. The basic idea of our method is that, if a parent gene is a transcription factor, its children may share a consensus motif in their promoter regions of the DNA sequences. Our method detects consensus motifs based on the structure of the estimated network, then re-estimates the network using the result of the motif detection. We continue this iteration until the network becomes stable. To show the effectiveness of our method, we conducted Monte Carlo simulations and applied our method to Saccharomyces cerevisiae data as a real application.

Original languageEnglish
JournalBioinformatics
Volume19
Issue numberSUPPL. 2
DOIs
Publication statusPublished - Dec 1 2003

Fingerprint

Gene Networks
Gene Regulatory Networks
DNA sequences
Bayesian networks
Bayesian Model
Microarrays
Gene Expression Data
Bayesian Networks
Promoter
Gene expression
Network Model
Genes
Gene Expression
Transcription factors
Genetic Promoter Regions
Yeast
Statistical methods
Transcription Factors
DNA Sequence
Monte Carlo Method

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. / Tamada, Yoshinori; Kim, Sun Yong; Bannai, Hideo; Imoto, Seiya; Tashiro, Kosuke; Kuhara, Satoru; Miyano, Satoru.

In: Bioinformatics, Vol. 19, No. SUPPL. 2, 01.12.2003.

Research output: Contribution to journalArticle

Tamada, Yoshinori ; Kim, Sun Yong ; Bannai, Hideo ; Imoto, Seiya ; Tashiro, Kosuke ; Kuhara, Satoru ; Miyano, Satoru. / Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. In: Bioinformatics. 2003 ; Vol. 19, No. SUPPL. 2.
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