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ATHENA: the analysis tool for heritable and environmental network associations
Emily R Holzinger1, Scott M Dudek, Alex T Frase
1Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA and Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, PA, USA.
Bioinformatics (Oxford, England)
|October 24, 2013
Summary
A new software, ATHENA, analyzes genetic data to uncover complex trait associations, addressing unexplained heritability. It uses machine learning to build predictive models from genetic and gene expression data.
Area of Science:
- Genetics and Bioinformatics
- Computational Biology
- Systems Biology
Background:
- High-throughput technologies enable genetic studies of complex human traits.
- Genome-wide association studies (GWAS) explain only a fraction of heritability.
- Complex etiologies, including gene-gene/environment interactions and regulatory layers, may be involved.
Purpose of the Study:
- To develop computational tools for analyzing large datasets to detect complex disease susceptibility models.
- To introduce the Analysis Tool for Heritable and Environmental Network Associations (ATHENA) software package.
- To demonstrate ATHENA's utility in identifying complex prediction models using simulated and biological data.
Main Methods:
- ATHENA integrates variable filtering with machine learning techniques.
- Analyzes high-throughput categorical (SNP) and quantitative (gene expression) predictor variables.
- Generates multivariable models for predicting categorical (disease status) or quantitative (cholesterol levels) outcomes.
Main Results:
- ATHENA successfully identified complex prediction models using SNP and gene expression data.
- Demonstrated the software's capability to handle large, multi-dimensional biological datasets.
- Highlighted the flexibility of ATHENA for incorporating diverse high-throughput data types.
Conclusions:
- ATHENA provides a robust computational approach to explore genetic architecture of complex traits.
- The software facilitates the discovery of novel genetic associations and predictive models.
- ATHENA is freely available, supporting broader research in genetic epidemiology and personalized medicine.
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