title: Analyzing Illumina Gene Expression Microarray Data Obtained From Human Whole Blood Cell and Blood Monocyte Samples.
abstract: Microarray profiling of gene expression is widely applied to studies in molecular biology and functional genomics. Experimental and technical variations make not only the statistical analysis of single studies but also meta-analyses of different studies very challenging. Here, we describe the analytical steps required to substantially reduce the variations of gene expression data without affecting true effect sizes. A software pipeline has been established using gene expression data from a total of 3358 whole blood cell and blood monocyte samples, all from three German population-based cohorts, measured on the Illumina HumanHT-12 v3 BeadChip array. In summary, adjustment for a few selected technical factors greatly improved reliability of gene expression analyses. Such adjustments are particularly required for meta-analyses of different studies.
authors.affiliation: Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany. ateumer@uni-greifswald.de.|Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Fleischmannstraße 8, Greifswald, Germany. ateumer@uni-greifswald.de.
authors.forename: Alexander
authors.initials: A
authors.lastname: Teumer
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Fleischmannstraße 8, Greifswald, Germany.|The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 10029, New York, NY, USA.|The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, 10029, New York, NY, USA.
authors.forename: Claudia
authors.initials: C
authors.lastname: Schurmann
authors.affiliation: Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.|DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany.
authors.forename: Arne
authors.initials: A
authors.lastname: Schillert
authors.affiliation: Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany.|German Research Center for Environmental Health, Neuherberg, Germany.|Institute of Human Genetics, Technical University Munich, Munich, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Schramm
authors.affiliation: Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.|DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany.|Center for Clinical Trials, University of Lübeck, Lübeck, Germany.|School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa.
authors.forename: Andreas
authors.initials: A
authors.lastname: Ziegler
authors.affiliation: Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany.|German Research Center for Environmental Health, Neuherberg, Germany.|Institute of Human Genetics, Technical University Munich, Munich, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Prokisch
mesh_terms: D000704:Analysis of Variance; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008297:Male; D009000:Monocytes / Q000378:metabolism*; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010641:Phenotype; D011786:Quality Control; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification; D013194:Staining and Labeling
chemical_list: D012333:RNA, Messenger
keywords: BeadChip; Gene expression analysis; Human monocytes; Human whole blood cells; ILLUMINA HumanHT-12; Microarray; Transcriptomics