title: Meta-eQTL: a tool set for flexible eQTL meta-analysis.
abstract: BACKGROUND
  Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also necessary for ChrX eQTL discovery.
  
  
  RESULTS
  We developed a novel tool, meta-eqtl, for fast eQTL meta-analysis of arbitrary sample size and arbitrary number of datasets. Further, this tool accommodates versatile modeling, eg. non-parametric model and mixed effect models. In addition, meta-eqtl readily handles calculation of chrX eQTLs.
  
  
  CONCLUSIONS
  We demonstrated and validated meta-eqtl as fast and comprehensive tool to meta-analyze multiple datasets and ChrX eQTL discovery. Meta-eqtl is a set of command line utilities written in R, with some computationally intensive parts written in C. The software runs on Linux platforms and is designed to intelligently adapt to high performance computing (HPC) cluster. We applied the novel tool to liver and adipose tissue data, and revealed eSNPs underlying diabetes GWAS loci.
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. antonio.dinarzo@mssm.edu.|Icahn Institute of Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai, New York, NY, USA. antonio.dinarzo@mssm.edu.
authors.forename: Antonio Fabio
authors.initials: AF
authors.lastname: Di Narzo
authors.affiliation: College of Electronics and Information Engineering, CIMS Research Center, Tongji University, Shanghai, China. hxchengtj@gmail.com.
authors.forename: Haoxiang
authors.initials: H
authors.lastname: Cheng
authors.affiliation: School of Software Engineering and The Advanced Institute of Translational Medicine, Tongji University, Shanghai, China. jwlu33@hotmail.com.|Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China. jwlu33@hotmail.com.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Lu
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. ke.hao@mssm.edu.|Icahn Institute of Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai, New York, NY, USA. ke.hao@mssm.edu.|Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China. ke.hao@mssm.edu.
authors.forename: Ke
authors.initials: K
authors.lastname: Hao
mesh_terms: D041321:Chromosomes, Human, X / Q000235:genetics; D003920:Diabetes Mellitus / Q000235:genetics; D054637:Dual-Specificity Phosphatases / Q000235:genetics; D005260:Female; D055106:Genome-Wide Association Study; D006801:Humans; D008099:Liver / Q000378:metabolism; D008297:Male; D015201:Meta-Analysis as Topic; D054639:Mitogen-Activated Protein Kinase Phosphatases / Q000235:genetics; D008962:Models, Theoretical; D040641:Quantitative Trait Loci; D012984:Software
chemical_list: D054639:Mitogen-Activated Protein Kinase Phosphatases; C104821:DUSP9 protein, human; D054637:Dual-Specificity Phosphatases