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Molecules 2018, 23(8), 2055; https://doi.org/10.3390/molecules23082055

Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures

1
Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China
2
Department of Automation, College of Intelligent Manufacturing and Automation, Henan University of Animal Husbandry and Economy, Zhengzhou 450011, China
3
Shaanxi Engineering Research Center of Medical and Health Big Data, School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an 710049, China
4
Department of Network Technology, College of Intelligent Manufacturing and Automation, Henan University of Animal Husbandry and Economy, Zhengzhou 450011, China
*
Authors to whom correspondence should be addressed.
Academic Editors: Xiangxiang Zeng, Alfonso Rodríguez-Patón and Quan Zou
Received: 25 June 2018 / Revised: 2 August 2018 / Accepted: 7 August 2018 / Published: 16 August 2018
(This article belongs to the Special Issue Molecular Computing and Bioinformatics)
Full-Text   |   PDF [8019 KB, uploaded 18 August 2018]   |  

Abstract

Gene fusion structure is a class of common somatic mutational events in cancer genomes, which are often formed by chromosomal mutations. Identifying the driver gene(s) in a fusion structure is important for many downstream analyses and it contributes to clinical practices. Existing computational approaches have prioritized the importance of oncogenes by incorporating prior knowledge from gene networks. However, different methods sometimes suffer different weaknesses when handling gene fusion data due to multiple issues such as fusion gene representation, network integration, and the effectiveness of the evaluation algorithms. In this paper, Synstable Fusion (SYN), an algorithm for computationally evaluating the fusion genes, is proposed. This algorithm uses network-based strategy by incorporating gene networks as prior information, but estimates the driver genes according to the destructiveness hypothesis. This hypothesis balances the two popular evaluation strategies in the existing studies, thereby providing more comprehensive results. A machine learning framework is introduced to integrate multiple networks and further solve the conflicting results from different networks. In addition, a synchronous stability model is established to reduce the computational complexity of the evaluation algorithm. To evaluate the proposed algorithm, we conduct a series of experiments on both artificial and real datasets. The results demonstrate that the proposed algorithm performs well on different configurations and is robust when altering the internal parameter settings. View Full-Text
Keywords: gene fusion data; gene susceptibility prioritization; evaluating driver partner; gene networks gene fusion data; gene susceptibility prioritization; evaluating driver partner; gene networks
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Xu, M.; Zhao, Z.; Zhang, X.; Gao, A.; Wu, S.; Wang, J. Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures. Molecules 2018, 23, 2055.

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