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Estimating genomic coexpression networks using first-order conditional independence.

Publication ,  Journal Article
Magwene, PM; Kim, J
Published in: Genome Biol
2004

We describe a computationally efficient statistical framework for estimating networks of coexpressed genes. This framework exploits first-order conditional independence relationships among gene-expression measurements to estimate patterns of association. We use this approach to estimate a coexpression network from microarray gene-expression measurements from Saccharomyces cerevisiae. We demonstrate the biological utility of this approach by showing that a large number of metabolic pathways are coherently represented in the estimated network. We describe a complementary unsupervised graph search algorithm for discovering locally distinct subgraphs of a large weighted graph. We apply this algorithm to our coexpression network model and show that subgraphs found using this approach correspond to particular biological processes or contain representatives of distinct gene families.

Duke Scholars

Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

2004

Volume

5

Issue

12

Start / End Page

R100

Location

England

Related Subject Headings

  • Saccharomyces cerevisiae
  • Oligonucleotide Array Sequence Analysis
  • Models, Statistical
  • Models, Genetic
  • Genomics
  • Genome, Fungal
  • Gene Expression
  • Cluster Analysis
  • Carbohydrate Metabolism
  • Bioinformatics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Magwene, P. M., & Kim, J. (2004). Estimating genomic coexpression networks using first-order conditional independence. Genome Biol, 5(12), R100. https://doi.org/10.1186/gb-2004-5-12-r100
Magwene, Paul M., and Junhyong Kim. “Estimating genomic coexpression networks using first-order conditional independence.Genome Biol 5, no. 12 (2004): R100. https://doi.org/10.1186/gb-2004-5-12-r100.
Magwene, Paul M., and Junhyong Kim. “Estimating genomic coexpression networks using first-order conditional independence.Genome Biol, vol. 5, no. 12, 2004, p. R100. Pubmed, doi:10.1186/gb-2004-5-12-r100.

Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

2004

Volume

5

Issue

12

Start / End Page

R100

Location

England

Related Subject Headings

  • Saccharomyces cerevisiae
  • Oligonucleotide Array Sequence Analysis
  • Models, Statistical
  • Models, Genetic
  • Genomics
  • Genome, Fungal
  • Gene Expression
  • Cluster Analysis
  • Carbohydrate Metabolism
  • Bioinformatics