title: Graph-regularized dual Lasso for robust eQTL mapping.
abstract: BACKGROUND
  As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage such network information. Despite their success, existing methods have three common limitations: (i) a preprocessing step is usually needed to cluster the networks; (ii) the incompleteness of the networks and the noise in them are not considered; (iii) other available information, such as location of genetic markers and pathway information are not integrated.
  
  
  RESULTS
  To address the limitations of the existing methods, we propose Graph-regularized Dual Lasso (GDL), a robust approach for eQTL mapping. GDL integrates the correlation structures among genetic markers and traits simultaneously. It also takes into account the incompleteness of the networks and is robust to the noise. GDL utilizes graph-based regularizers to model the prior networks and does not require an explicit clustering step. Moreover, it enables further refinement of the partial and noisy networks. We further generalize GDL to incorporate the location of genetic makers and gene-pathway information. We perform extensive experimental evaluations using both simulated and real datasets. Experimental results demonstrate that the proposed methods can effectively integrate various available priori knowledge and significantly outperform the state-of-the-art eQTL mapping methods.
  
  
  BACKGROUND
  Software for both C++ version and Matlab version is available at http://www.cs.unc.edu/∼weicheng/.
authors.affiliation: Department of Computer Science, UNC at Chapel Hill, Chapel Hill, NC 27599, Department of EECS, Case Western Reserve University, OH 44106, USA Department of Mathematics, University of Science and Technology of China, Hefei 23002, China and Department of Computer Science, University of California, Los Angeles, CA 90095, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Cheng
authors.affiliation: Department of Computer Science, UNC at Chapel Hill, Chapel Hill, NC 27599, Department of EECS, Case Western Reserve University, OH 44106, USA Department of Mathematics, University of Science and Technology of China, Hefei 23002, China and Department of Computer Science, University of California, Los Angeles, CA 90095, USA.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Computer Science, UNC at Chapel Hill, Chapel Hill, NC 27599, Department of EECS, Case Western Reserve University, OH 44106, USA Department of Mathematics, University of Science and Technology of China, Hefei 23002, China and Department of Computer Science, University of California, Los Angeles, CA 90095, USA.
authors.forename: Zhishan
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Department of Computer Science, UNC at Chapel Hill, Chapel Hill, NC 27599, Department of EECS, Case Western Reserve University, OH 44106, USA Department of Mathematics, University of Science and Technology of China, Hefei 23002, China and Department of Computer Science, University of California, Los Angeles, CA 90095, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Department of Computer Science, UNC at Chapel Hill, Chapel Hill, NC 27599, Department of EECS, Case Western Reserve University, OH 44106, USA Department of Mathematics, University of Science and Technology of China, Hefei 23002, China and Department of Computer Science, University of California, Los Angeles, CA 90095, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D016000:Cluster Analysis; D015870:Gene Expression; D053263:Gene Regulatory Networks; D005819:Genetic Markers; D016014:Linear Models; D020641:Polymorphism, Single Nucleotide; D025941:Protein Interaction Mapping; D040641:Quantitative Trait Loci; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism
chemical_list: D005819:Genetic Markers