Genome-wide integrative analysis identified SNP-miRNA-mRNA interaction networks in peripheral blood mononuclear cells

References

• Brennecke J , HipfnerDR , StarkA , RussellRB , CohenSM . Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila . Cell113 ( 1 ), 25 – 36 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Wilfred BR , WangWX , NelsonPT . Energizing miRNA research: a review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways . Mol. Genet. Metab.91 ( 3 ), 209 – 217 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Hydbring P , Badalian-VeryG . Clinical applications of microRNAs . F1000Res2 , 136 ( 2013 ).
   PubMedGoogle Scholar
• Lin SP , YeS , ChenXHet al. Increased expression of microRNA-21 in peripheral blood mediates the down-regulation of IFN-gamma and increases the prevalence of stroke-associated infection . J. Neurol. Sci.366 , 235 – 239 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Ambros V . The functions of animal microRNAs . Nature431 ( 7006 ), 350 – 355 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Bartel DP . MicroRNAs: genomics, biogenesis, mechanism, and function . Cell116 ( 2 ), 281 – 297 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Pickrell JK , MarioniJC , PaiAAet al. Understanding mechanisms underlying human gene expression variation with RNA sequencing . Nature464 ( 7289 ), 768 – 772 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Heinig M , PetrettoE , WallaceCet al. A trans-acting locus regulates an anti-viral expression network and Type 1 diabetes risk . Nature467 ( 7314 ), 460 – 464 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Veyrieras JB , KudaravalliS , KimSYet al. High-resolution mapping of expression-QTLs yields insight into human gene regulation . PLoS Genet.4 ( 10 ), e1000214 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Zeller T , WildP , SzymczakSet al. Genetics and beyond – the transcriptome of human monocytes and disease susceptibility . PLoS ONE5 ( 5 ), e10693 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Small KS , HedmanAK , GrundbergEet al. Identification of an imprinted master trans-regulator at the KLF14 locus related to multiple metabolic phenotypes . Nat. Genet.43 ( 6 ), 561 – 564 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Grundberg E , SmallKS , HedmanAKet al. Mapping cis- and trans-regulatory effects across multiple tissues in twins . Nat. Genet.44 ( 10 ), 1084 – 1089 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Westra HJ , PetersMJ , EskoTet al. Systematic identification of trans eQTLs as putative drivers of known disease associations . Nat. Genet.45 ( 10 ), 1238 – 1243 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Fadista J , VikmanP , LaaksoEOet al. Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism . Proc. Natl. Acad. Sci. USA111 ( 38 ), 13924 – 13929 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Kumar V , WestraHJ , KarjalainenJet al. Human disease-associated genetic variation impacts large intergenic non-coding RNA expression . PLoS Genet.9 ( 1 ), e1003201 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Luijk R , GoemanJJ , SlagboomEP , HeijmansBT , Van ZwetEW . An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs . Bioinformatics31 ( 3 ), 340 – 345 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Wagner JR , BuscheS , GeB , KwanT , PastinenT , BlanchetteM . The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts . Genome Biol.15 ( 2 ), R37 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Civelek M , HagopianR , PanCet al. Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits . Hum. Mol. Genet.22 ( 15 ), 3023 – 3037 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Huan T , RongJ , LiuCet al. Genome-wide identification of microRNA expression quantitative trait loci . Nat. Commun.6 , 6601 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Mccarthy MI , HirschhornJN . Genome-wide association studies: potential next steps on a genetic journey . Hum. Mol. Genet.17 ( R2 ), R156 – R165 ( 2008 ).
   PubMedGoogle Scholar
• Altshuler D , DalyMJ , LanderES . Genetic mapping in human disease . Science322 ( 5903 ), 881 – 888 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Lettre G , RiouxJD . Autoimmune diseases: insights from genome-wide association studies . Hum. Mol. Genet.17 ( R2 ), R116 – R121 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Lei SF , PapasianCJ , DengHW . Polymorphisms in predicted miRNA binding sites and osteoporosis . J. Bone Miner Res.26 ( 1 ), 72 – 78 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Stegeman S , AmankwahE , KleinKet al. A large-scale analysis of genetic variants within putative miRNA binding sites in prostate cancer . Cancer Discov.5 ( 4 ), 368 – 379 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Ye Q , ZhaoX , XuKet al. Polymorphisms in lipid metabolism related miRNA binding sites and risk of metabolic syndrome . Gene528 ( 2 ), 132 – 138 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Chen LS , Emmert-StreibF , StoreyJD . Harnessing naturally randomized transcription to infer regulatory relationships among genes . Genome Biol.8 ( 10 ), R219 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Shabalin AA . Matrix eQTL: ultra fast eQTL analysis via large matrix operations . Bioinformatics28 ( 10 ), 1353 – 1358 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Huang T , CaiYD . An information-theoretic machine learning approach to expression QTL analysis . PLoS ONE8 ( 6 ), e67899 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Dayem Ullah AZ , LemoineNR , ChelalaC . SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update) . Nucleic Acids Res.40 ( Web Server issue ), W65 – W70 ( 2012 ).
   PubMedGoogle Scholar
• Dayem Ullah AZ , LemoineNR , ChelalaC . A practical guide for the functional annotation of genetic variations using SNPnexus . Brief Bioinform.14 ( 4 ), 437 – 447 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Xu Z , TaylorJA . SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies . Nucleic Acids Res.37 ( Web Server issue ), W600 – W605 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Su G , MorrisJH , DemchakB , BaderGD . Biological network exploration with Cytoscape 3 . Curr. Protoc. Bioinformatics47 , 8.13.1 – 8.13.24 ( 2014 ).
   PubMedGoogle Scholar
• Genomes Project C , AbecasisGR , AutonAet al. An integrated map of genetic variation from 1092 human genomes . Nature491 ( 7422 ), 56 – 65 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Millstein J , ZhangB , ZhuJ , SchadtEE . Disentangling molecular relationships with a causal inference test . BMC Genet.10 , 23 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Huang Da W , ShermanBT , LempickiRA . Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists . Nucleic Acids Res.37 ( 1 ), 1 – 13 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Huang Da W , ShermanBT , LempickiRA . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources . Nat. Protoc.4 ( 1 ), 44 – 57 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Siddle KJ , DeschampsM , TailleuxLet al. A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection . Genome Res.24 ( 5 ), 850 – 859 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Borel C , DeutschS , LetourneauAet al. Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts . Genome Res.21 ( 1 ), 68 – 73 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Gamazon ER , ZiliakD , ImHKet al. Genetic architecture of microRNA expression: implications for the transcriptome and complex traits . Am. J. Hum. Genet.90 ( 6 ), 1046 – 1063 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Dimas AS , DeutschS , StrangerBEet al. Common regulatory variation impacts gene expression in a cell type-dependent manner . Science325 ( 5945 ), 1246 – 1250 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Deng FY , LeiSF , ZhangYH , ZhangZL , GuoYF . Functional relevance for associations between genetic variants and systemic lupus erythematosus . PLoS One8 ( 1 ), e53037 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Deng FY , LeiSF , ZhuH , ZhangYH , ZhangZL . Integrative analyses for functional mechanisms underlying associations for rheumatoid arthritis . J. Rheumatol.40 ( 7 ), 1063 – 1068 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Lim LP , LauNC , Garrett-EngelePet al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs . Nature433 ( 7027 ), 769 – 773 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Mercer TR , DingerME , MattickJS . Long non-coding RNAs: insights into functions . Nat. Rev. Genet.10 ( 3 ), 155 – 159 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Wang KC , ChangHY . Molecular mechanisms of long noncoding RNAs . Mol. Cell43 ( 6 ), 904 – 914 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Karin M . Too many transcription factors: positive and negative interactions . New Biol.2 ( 2 ), 126 – 131 ( 1990 ).
   PubMedGoogle Scholar
• Morozova N , ZinovyevA , NonneN , PritchardLL , GorbanAN , Harel-BellanA . Kinetic signatures of microRNA modes of action . RNA18 ( 9 ), 1635 – 1655 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Cook-Sather SD , LiJ , GoebelTK , SussmanEM , RehmanMA , HakonarsonH . TAOK3, a novel genome-wide association study locus associated with morphine requirement and postoperative pain in a retrospective pediatric day surgery population . Pain155 ( 9 ), 1773 – 1783 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Comuzzie AG , ColeSA , LastonSLet al. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population . PLoS ONE7 ( 12 ), e51954 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Abdelmohsen K , SrikantanS , YangXet al. Ubiquitin-mediated proteolysis of HuR by heat shock . The EMBO J.28 ( 9 ), 1271 – 1282 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Lui WO , PourmandN , PattersonBK , FireA . Patterns of known and novel small RNAs in human cervical cancer . Cancer Res67 ( 13 ), 6031 – 6043 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Zhang PP , WangXL , ZhaoWet al. DNA methylation-mediated repression of miR-941 enhances lysine (K)-specific demethylase 6B expression in hepatoma cells . J. Biol. Chem.289 ( 35 ), 24724 – 24735 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Hu HY , HeL , FominykhKet al. Evolution of the human-specific microRNA miR-941 . Nat. Commun.3 , 1145 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Stokowy T , EszlingerM , SwierniakMet al. Analysis options for high-throughput sequencing in miRNA expression profiling . BMC Res. Notes7 , 144 ( 2014 ).
   PubMedGoogle Scholar
• Schrijver WA , Van DiestPJ , MoelansCB , Dutch Distant Breast Cancer Metastases Consortium . Unravelling site-specific breast cancer metastasis: a microRNA expression profiling study . Oncotarget doi:10.18632/oncotarget.13623 ( 2016 ) ( Epub ahead of print ).
   Google Scholar
• Shi C , HuangF , GuXet al. Adipogenic miRNA and meta-signature miRNAs involved in human adipocyte differentiation and obesity . Oncotarget7 ( 26 ), 40830 – 40845 ( 2016 ).
   PubMedGoogle Scholar
• Yilmaz SG , ErdalME , OzgeAA , SungurMA . Can peripheral MicroRNA expression data serve as epigenomic (upstream) biomarkers of Alzheimer’s disease?OMICS20 ( 8 ), 456 – 461 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Wang W , SunG , ZhangL , ShiL , ZengY . Circulating microRNAs as novel potential biomarkers for early diagnosis of acute stroke in humans . J. Stroke Cerebrovasc. Dis.23 ( 10 ), 2607 – 2613 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Ober C , LoiselDA , GiladY . Sex-specific genetic architecture of human disease . Nat. Rev. Genet.9 ( 12 ), 911 – 922 ( 2008 ).
   PubMed Web of Science ®Google Scholar