ArticleBMC genomics2005
A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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Who cites it
74 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies.BMC neurology · 2017Pooled it
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- Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network.PloS one · 2019Article
- Bifidobacterium breve UCC2003 Employs Multiple Transcriptional Regulators To Control Metabolism of Particular Human Milk Oligosaccharides.Applied and environmental microbiology · 2018Article
- Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve.Nucleic acids research · 2018Article
- Characterizing a thermostable Cas9 for bacterial genome editing and silencing.Nature communications · 2017Article
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- Efficient Genome Editing of a Facultative Thermophile Using Mesophilic spCas9.ACS synthetic biology · 2017Article
- CodY Regulates Thiol Peroxidase Expression as Part of the Pneumococcal Defense Mechanism against HFrontiers in cellular and infection microbiology · 2017Article
- Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation.Frontiers in microbiology · 2017Article
- Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways.Scientific reports · 2016Article
- Glycosulfatase-Encoding Gene Cluster in Bifidobacterium breve UCC2003.Applied and environmental microbiology · 2016Article
- Regulation of Cell Wall Plasticity by Nucleotide Metabolism in Lactococcus lactis.The Journal of biological chemistry · 2016Article
- Transcriptome analysis of Streptococcus pneumoniae D39 in the presence of cobalt.Genomics data · 2015Article
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- Transcriptional profiling of UlaR-regulated genes in Streptococcus pneumoniae.Genomics data · 2015Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed.
resultsA number of validation experiments were performed on Lactococcus lactis IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance.
conclusionEven in cases where 90% of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days), the CV was at an acceptable 25%. Clustering experiments showed that trends can be reliably detected also from genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.
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