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Open Access Research

Feature ranking based on synergy networks to identify prognostic markers in DPT-1

Amin Ahmadi Adl1, Xiaoning Qian12*, Ping Xu3, Kendra Vehik3 and Jeffrey P Krischer3

Author Affiliations

1 Department of Computer Science and Engineering, University of South Florida, Tampa, FL, 33620, USA

2 Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, 77843, USA

3 Department of Pediatrics, College of Medicine, University of South Florida, Tampa, FL, 33613, USA

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EURASIP Journal on Bioinformatics and Systems Biology 2013, 2013:12  doi:10.1186/1687-4153-2013-12

Published: 19 September 2013

Abstract

Interaction among different risk factors plays an important role in the development and progress of complex disease, such as diabetes. However, traditional epidemiological methods often focus on analyzing individual or a few ‘essential’ risk factors, hopefully to obtain some insights into the etiology of complex disease. In this paper, we propose a systematic framework for risk factor analysis based on a synergy network, which enables better identification of potential risk factors that may serve as prognostic markers for complex disease. A spectral approximate algorithm is derived to solve this network optimization problem, which leads to a new network-based feature ranking method that improves the traditional feature ranking by taking into account the pairwise synergistic interactions among risk factors in addition to their individual predictive power. We first evaluate the performance of our method based on simulated datasets, and then, we use our method to study immunologic and metabolic indices based on the Diabetes Prevention Trial-Type 1 (DPT-1) study that may provide prognostic and diagnostic information regarding the development of type 1 diabetes. The performance comparison based on both simulated and DPT-1 datasets demonstrates that our network-based ranking method provides prognostic markers with higher predictive power than traditional analysis based on individual factors.

Keywords:
DPT-1; Type 1 diabetes; Biomarker identification; Interaction; Synergy network; Feature ranking