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Hypergraph Supervised Search for Inferring Multiple Epistatic Interactions with Different Orders

  • Junliang Shang
  • Yan Sun
  • Yun Fang
  • Shengjun Li
  • Jin-Xing Liu
  • Yuanke Zhang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9226)

Abstract

Nonlinear interactive effects of Single Nucleotide Polymorphisms (SNPs), namely, epistatic interactions, have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for their detection, most only focus on the detection of pairwise epistatic interactions. In this study, a Hypergraph Supervised Search (HgSS) is developed based on the co-information measure for inferring multiple epistatic interactions with different orders at a substantially reduced time cost. The co-information measure is employed to exhaustively quantify the interaction effects of low order SNP combinations, as well as the main effects of SNPs. Then, highly suspected SNP combinations and SNPs are used to construct a hypergraph. By deeply analyzing the hypergraph, some clues for better understanding the genetic architecture of complex diseases could be revealed. Experiments are performed on both simulation and real data sets. Results show that HgSS is promising in inferring multiple epistatic interactions with different orders.

Keywords

Epistatic interactions Single nucleotide polymorphisms (SNPs) Genome-wide association study Hypergraph Genetic interaction network 

Notes

Acknowledgments

This work was supported by the Scientific Research Reward Foundation for Excellent Young and Middle-age Scientists of Shandong Province (BS2014DX004), the Science and Technology Planning Project of Qufu Normal University (xkj201410), the Opening Laboratory Fund of Qufu Normal University (sk201416), the Scientific Research Foundation of Qufu Normal University (BSQD20130119), the Project of Shandong Province Higher Educational Science and Technology Program (J13LN31), the Award Foundation Project of Excellent Young Scientists in Shandong Province (BS2014DX005), the Shenzhen Municipal Science and Technology Innovation Council (JCYJ20140417172417174), the Shandong Provincial Natural Science Foundation (ZR2013FL016), the China Postdoctoral Science Foundation Funded Project (2014M560264).

Conflict of Interests

The authors declare that there is no conflict of interests regarding the publication of this paper.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Junliang Shang
    • 1
  • Yan Sun
    • 1
  • Yun Fang
    • 1
  • Shengjun Li
    • 1
  • Jin-Xing Liu
    • 1
    • 2
  • Yuanke Zhang
    • 1
  1. 1.School of Information Science and EngineeringQufu Normal UniversityRizhaoChina
  2. 2.Bio-Computing Research Center, Shenzhen Graduate SchoolHarbin Institute of TechnologyShenzhenChina

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