Paper Info
Title
HC-HDSD: A method of hypergraph construction and high-density subgraph detection for inferring high-order epistatic interactions.
Abstract
Detecting epistatic interactions, or nonlinear interactive effects of Single Nucleotide Polymorphisms (SNPs), has gained increasing attention in explaining the “missing heritability” of complex diseases. Though much work has been done in mapping SNPs underlying diseases, most of them constrain to 2-order epistatic interactions. In this paper, a method of hypergraph construction and high-density subgraph detection, named HC-HDSD, is proposed for detecting high-order epistatic interactions. The hypergraph is constructed by low-order epistatic interactions that identified using the normalized co-information measure and the exhaustive search. The hypergraph consists of two types of vertices: real ones representing main effects of SNPs and virtual ones denoting interactive effects of epistatic interactions. Then, both maximal clique centrality algorithm and near-clique mining algorithm are employed to detect high-density subgraphs from the constructed hypergraph. These high-density subgraphs are inferred as high-order epistatic interactions in the HC-HDSD. Experiments are performed on several simulation data sets, results of which show that HC-HDSD is promising in inferring high-order epistatic interactions while substantially reducing the computation cost. In addition, the application of HC-HDSD on a real Age-related Macular Degeneration (AMD) data set provides several new clues for the exploration of causative factors of AMD.
Year
DOI
Venue
2019
10.1016/j.compbiolchem.2018.11.031
Computational Biology and Chemistry
Keywords
Field
DocType
Epistatic interactions,Single nucleotide polymorphisms (SNPs),Co-information,Hypergraph,High-density subgraph
Data set,Missing heritability problem,Brute-force search,Clique,Biology,Vertex (geometry),Epistasis,Hypergraph,Centrality,Theoretical computer science,Genetics
Journal
Volume
ISSN
Citations 
78
1476-9271
0
PageRank 
References 
Authors
0.34
11
5
Name
Order
Citations
PageRank
Qian Ding1855.31
Junliang Shang24214.78
Yingxia Sun341.44
Xuan Wang401.01
Liu Jin-Xing54016.11