title: Inference of SNP-gene regulatory networks by integrating gene expressions and genetic perturbations.
abstract: In order to elucidate the overall relationships between gene expressions and genetic perturbations, we propose a network inference method to infer gene regulatory network where single nucleotide polymorphism (SNP) is involved as a regulator of genes. In the most of the network inferences named as SNP-gene regulatory network (SGRN) inference, pairs of SNP-gene are given by separately performing expression quantitative trait loci (eQTL) mappings. In this paper, we propose a SGRN inference method without predefined eQTL information assuming a gene is regulated by a single SNP at most. To evaluate the performance, the proposed method was applied to random data generated from synthetic networks and parameters. There are three main contributions. First, the proposed method provides both the gene regulatory inference and the eQTL identification. Second, the experimental results demonstrated that integration of multiple methods can produce competitive performances. Lastly, the proposed method was also applied to psychiatric disorder data in order to explore how the method works with real data.
authors.affiliation: Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA.
authors.forename: Dong-Chul
authors.identifier: 0000-0003-2461-8705
authors.initials: DC
authors.lastname: Kim
authors.affiliation: Beijing Genomics Institution at Wuhan, Wuhan 430075, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 66012, USA.
authors.forename: Chunyu
authors.initials: C
authors.lastname: Liu
authors.affiliation: Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA.
authors.forename: Jean
authors.initials: J
authors.lastname: Gao
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*