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    Learning gene regulatory networks from gene expression data using weighted consensus

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    Type
    Article
    Authors
    Fujii, Chisato cc
    Kuwahara, Hiroyuki cc
    Yu, Ge
    Guo, Lili
    Gao, Xin cc
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    KAUST Grant Number
    URF/1/1976-04
    Date
    2016-08-25
    Online Publication Date
    2016-08-25
    Print Publication Date
    2017-01
    Permanent link to this record
    http://hdl.handle.net/10754/622306
    
    Metadata
    Show full item record
    Abstract
    An accurate determination of the network structure of gene regulatory systems from high-throughput gene expression data is an essential yet challenging step in studying how the expression of endogenous genes is controlled through a complex interaction of gene products and DNA. While numerous methods have been proposed to infer the structure of gene regulatory networks, none of them seem to work consistently over different data sets with high accuracy. A recent study to compare gene network inference methods showed that an average-ranking-based consensus method consistently performs well under various settings. Here, we propose a linear programming-based consensus method for the inference of gene regulatory networks. Unlike the average-ranking-based one, which treats the contribution of each individual method equally, our new consensus method assigns a weight to each method based on its credibility. As a case study, we applied the proposed consensus method on synthetic and real microarray data sets, and compared its performance to that of the average-ranking-based consensus and individual inference methods. Our results show that our weighted consensus method achieves superior performance over the unweighted one, suggesting that assigning weights to different individual methods rather than giving them equal weights improves the accuracy. © 2016 Elsevier B.V.
    Citation
    Fujii C, Kuwahara H, Yu G, Guo L, Gao X (2017) Learning gene regulatory networks from gene expression data using weighted consensus. Neurocomputing 220: 23–33. Available: http://dx.doi.org/10.1016/j.neucom.2016.02.087.
    Sponsors
    This publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No URF/1/1976-04. This research made use of the resources of the computer clusters at KAUST.
    Publisher
    Elsevier BV
    Journal
    Neurocomputing
    DOI
    10.1016/j.neucom.2016.02.087
    Additional Links
    http://www.sciencedirect.com/science/article/pii/S092523121630916X
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.neucom.2016.02.087
    Scopus Count
    Collections
    Articles; Computer Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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