Classification of microarray data using gene networks

BackgroundMicroarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often difficult. Currently, the standard approach is to map a posteriori the results onto gene networks in order to elucidate the functions perturbed at the level of pathways. However, integrating a priori knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation.ResultsWe propose a method to integrate a priori the knowledge of a gene network in the analysis of gene expression data. The approach is based on the spectral decomposition of gene expression profiles with respect to the eigenfunctions of the graph, resulting in an attenuation of the high-frequency components of the expression profiles with respect to the topology of the graph. We show how to derive unsupervised and supervised classification algorithms of expression profiles, resulting in classifiers with biological relevance. We illustrate the method with the analysis of a set of expression profiles from irradiated and non-irradiated yeast strains.ConclusionIncluding a priori knowledge of a gene network for the analysis of gene expression data leads to good classification performance and improved interpretability of the results.

• Publication year

  2007

• Venue

  BMC Bioinformatics

• Publication date

  2007-02-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-8-35PMID 17270037PMCID 1797191
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Statistical Applications in Genetics and Molecular Biology Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data

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  2006cited by this paper
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  2005cited by this paper
• Bioinformatic methods for integrating whole-genome expression results into cellular networks.

  2005cited by this paper
• Systematic interpretation of genetic interactions using protein networks

  2005cited by this paper
• Pathways to the analysis of microarray data.

  2005cited by this paper
• Biological detection of low radiation doses by combining results of two microarray analysis methods.

  2004influential reference
• Filling gaps in a metabolic network using expression information

  2004cited by this paper
• The Elements of Statistical Learning: Data Mining, Inference, and Prediction

  2004cited by this paper
• Reactome: a knowledgebase of biological pathways

  2004cited by this paper
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  2004cited by this paper
• Pathway Activity Inference Using Microarray Data

  2004cited by this paper
• Modeling and Analysis of Heterogeneous Regulation in Biological Networks

  2004cited by this paper
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  2003cited by this paper
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  2003cited by this paper
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  2003cited by this paper
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  2003cited by this paper
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  2003influential reference
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  2003cited by this paper
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  2002cited by this paper
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  2002cited by this paper
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  2001cited by this paper
• Transcriptional induction of repair genes during slowing of replication in irradiated Saccharomyces cerevisiae.

  2001cited by this paper
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  2001cited by this paper
• Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits.

  2001cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data

  2000cited by this paper
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  1992cited by this paper
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