An effective framework for reconstructing gene regulatory networks from genetical genomics data
| Autor: | Sandra Heise, Robert J. Flassig, Steffen Klamt, Kai Sundmacher |
|---|---|
| Rok vydání: | 2012 |
| Předmět: |
Statistics and Probability
Genetics Genotype Quantitative Trait Loci Gene regulatory network Gene Expression Small sample Computational biology Genomics Saccharomyces cerevisiae Biology Biochemistry Genome Computer Science Applications Computational Mathematics Phenotype Computational Theory and Mathematics Graph (abstract data type) Gene Regulatory Networks Pruning (decision trees) Molecular Biology Genetical genomics Biological network Network analysis |
| Zdroj: | Bioinformatics (Oxford, England). 29(2) |
| ISSN: | 1367-4811 |
| Popis: | Motivation: Systems Genetics approaches, in particular those relying on genetical genomics data, put forward a new paradigm of large-scale genome and network analysis. These methods use naturally occurring multi-factorial perturbations (e.g. polymorphisms) in properly controlled and screened genetic crosses to elucidate causal relationships in biological networks. However, although genetical genomics data contain rich information, a clear dissection of causes and effects as required for reconstructing gene regulatory networks is not easily possible. Results: We present a framework for reconstructing gene regulatory networks from genetical genomics data where genotype and phenotype correlation measures are used to derive an initial graph which is subsequently reduced by pruning strategies to minimize false positive predictions. Applied to realistic simulated genetic data from a recent DREAM challenge, we demonstrate that our approach is simple yet effective and outperforms more complex methods (including the best performer) with respect to (i) reconstruction quality (especially for small sample sizes) and (ii) applicability to large data sets due to relatively low computational costs. We also present reconstruction results from real genetical genomics data of yeast. Availability: A MATLAB implementation (script) of the reconstruction framework is available at www.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html Contact: klamt@mpi-magdeburg.mpg.de |
| Databáze: | OpenAIRE |
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