Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium.
Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data...
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2012
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oai:doaj.org-article:7a4ce423b51c479ebf1edb414f618a962021-11-18T08:06:02ZAnalyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium.1932-620310.1371/journal.pone.0050938https://doaj.org/article/7a4ce423b51c479ebf1edb414f618a962012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23236413/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data preprocessing and the variability due to sample processing in whole blood cell and blood monocyte gene expression data, measured on the Illumina HumanHT-12 v3 BeadChip array.Gene expression signal intensities were similar after applying the log(2) or the variance-stabilizing transformation. In all cohorts, the first principal component (PC) explained more than 95% of the total variation. Technical factors substantially influenced signal intensity values, especially the Illumina chip assignment (33-48% of the variance), the RNA amplification batch (12-24%), the RNA isolation batch (16%), and the sample storage time, in particular the time between blood donation and RNA isolation for the whole blood cell samples (2-3%), and the time between RNA isolation and amplification for the monocyte samples (2%). White blood cell composition parameters were the strongest biological factors influencing the expression signal intensities in the whole blood cell samples (3%), followed by sex (1-2%) in both sample types. Known single nucleotide polymorphisms (SNPs) were located in 38% of the analyzed probe sequences and 4% of them included common SNPs (minor allele frequency >5%). Out of the tested SNPs, 1.4% significantly modified the probe-specific expression signals (Bonferroni corrected p-value<0.05), but in almost half of these events the signal intensities were even increased despite the occurrence of the mismatch. Thus, the vast majority of SNPs within probes had no significant effect on hybridization efficiency.In summary, adjustment for a few selected technical factors greatly improved reliability of gene expression analyses. Such adjustments are particularly required for meta-analyses.Claudia SchurmannKatharina HeimArne SchillertStefan BlankenbergMaren CarstensenMarcus DörrKarlhans EndlichStephan B FelixChristian GiegerHarald GrallertChristian HerderWolfgang HoffmannGeorg HomuthThomas IlligJochen KruppaThomas MeitingerChristian MüllerMatthias NauckAnnette PetersRainer RettigMichael RodenKonstantin StrauchUwe VölkerHenry VölzkeSimone WahlHenri WallaschofskiPhilipp S WildTanja ZellerAlexander TeumerHolger ProkischAndreas ZieglerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e50938 (2012) |
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Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Claudia Schurmann Katharina Heim Arne Schillert Stefan Blankenberg Maren Carstensen Marcus Dörr Karlhans Endlich Stephan B Felix Christian Gieger Harald Grallert Christian Herder Wolfgang Hoffmann Georg Homuth Thomas Illig Jochen Kruppa Thomas Meitinger Christian Müller Matthias Nauck Annette Peters Rainer Rettig Michael Roden Konstantin Strauch Uwe Völker Henry Völzke Simone Wahl Henri Wallaschofski Philipp S Wild Tanja Zeller Alexander Teumer Holger Prokisch Andreas Ziegler Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. |
| description |
Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data preprocessing and the variability due to sample processing in whole blood cell and blood monocyte gene expression data, measured on the Illumina HumanHT-12 v3 BeadChip array.Gene expression signal intensities were similar after applying the log(2) or the variance-stabilizing transformation. In all cohorts, the first principal component (PC) explained more than 95% of the total variation. Technical factors substantially influenced signal intensity values, especially the Illumina chip assignment (33-48% of the variance), the RNA amplification batch (12-24%), the RNA isolation batch (16%), and the sample storage time, in particular the time between blood donation and RNA isolation for the whole blood cell samples (2-3%), and the time between RNA isolation and amplification for the monocyte samples (2%). White blood cell composition parameters were the strongest biological factors influencing the expression signal intensities in the whole blood cell samples (3%), followed by sex (1-2%) in both sample types. Known single nucleotide polymorphisms (SNPs) were located in 38% of the analyzed probe sequences and 4% of them included common SNPs (minor allele frequency >5%). Out of the tested SNPs, 1.4% significantly modified the probe-specific expression signals (Bonferroni corrected p-value<0.05), but in almost half of these events the signal intensities were even increased despite the occurrence of the mismatch. Thus, the vast majority of SNPs within probes had no significant effect on hybridization efficiency.In summary, adjustment for a few selected technical factors greatly improved reliability of gene expression analyses. Such adjustments are particularly required for meta-analyses. |
| format |
article |
| author |
Claudia Schurmann Katharina Heim Arne Schillert Stefan Blankenberg Maren Carstensen Marcus Dörr Karlhans Endlich Stephan B Felix Christian Gieger Harald Grallert Christian Herder Wolfgang Hoffmann Georg Homuth Thomas Illig Jochen Kruppa Thomas Meitinger Christian Müller Matthias Nauck Annette Peters Rainer Rettig Michael Roden Konstantin Strauch Uwe Völker Henry Völzke Simone Wahl Henri Wallaschofski Philipp S Wild Tanja Zeller Alexander Teumer Holger Prokisch Andreas Ziegler |
| author_facet |
Claudia Schurmann Katharina Heim Arne Schillert Stefan Blankenberg Maren Carstensen Marcus Dörr Karlhans Endlich Stephan B Felix Christian Gieger Harald Grallert Christian Herder Wolfgang Hoffmann Georg Homuth Thomas Illig Jochen Kruppa Thomas Meitinger Christian Müller Matthias Nauck Annette Peters Rainer Rettig Michael Roden Konstantin Strauch Uwe Völker Henry Völzke Simone Wahl Henri Wallaschofski Philipp S Wild Tanja Zeller Alexander Teumer Holger Prokisch Andreas Ziegler |
| author_sort |
Claudia Schurmann |
| title |
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. |
| title_short |
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. |
| title_full |
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. |
| title_fullStr |
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. |
| title_full_unstemmed |
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. |
| title_sort |
analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/7a4ce423b51c479ebf1edb414f618a96 |
| work_keys_str_mv |
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