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Open Access Research

DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization

Sinan Erten1*, Gurkan Bebek234, Rob M Ewing235 and Mehmet Koyutürk123

Author Affiliations

1 Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA

2 Case Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA

3 Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA

4 Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA

5 Department of Genetics, Case Western Reserve University, Cleveland, OH, USA

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BioData Mining 2011, 4:19  doi:10.1186/1756-0381-4-19

Published: 24 June 2011

Abstract

Background

High-throughput molecular interaction data have been used effectively to prioritize candidate genes that are linked to a disease, based on the observation that the products of genes associated with similar diseases are likely to interact with each other heavily in a network of protein-protein interactions (PPIs). An important challenge for these applications, however, is the incomplete and noisy nature of PPI data. Information flow based methods alleviate these problems to a certain extent, by considering indirect interactions and multiplicity of paths.

Results

We demonstrate that existing methods are likely to favor highly connected genes, making prioritization sensitive to the skewed degree distribution of PPI networks, as well as ascertainment bias in available interaction and disease association data. Motivated by this observation, we propose several statistical adjustment methods to account for the degree distribution of known disease and candidate genes, using a PPI network with associated confidence scores for interactions. We show that the proposed methods can detect loosely connected disease genes that are missed by existing approaches, however, this improvement might come at the price of more false negatives for highly connected genes. Consequently, we develop a suite called DADA, which includes different uniform prioritization methods that effectively integrate existing approaches with the proposed statistical adjustment strategies. Comprehensive experimental results on the Online Mendelian Inheritance in Man (OMIM) database show that DADA outperforms existing methods in prioritizing candidate disease genes.

Conclusions

These results demonstrate the importance of employing accurate statistical models and associated adjustment methods in network-based disease gene prioritization, as well as other network-based functional inference applications. DADA is implemented in Matlab and is freely available at http://compbio.case.edu/dada/ webcite.