ArticleBMC genomics2005
Three microarray platforms: an analysis of their concordance in profiling gene expression.
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 42 papers, 1 of them a synthesis that pooled it.
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Who cites it
42 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A cross-laboratory comparison of expression profiling data from normal human postmortem brain.Neuroscience · 2010Pooled it
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- A quantitative model of transcriptional regulation reveals the influence of binding location on expression.PLoS computational biology · 2010Article
- Microarray probes and probe sets.Frontiers in bioscience (Elite edition) · 2010Review
- Phytoremediation and phytosensing of chemical contaminants, RDX and TNT: identification of the required target genes.Functional & integrative genomics · 2009Article
- Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes.BMC genomics · 2009Article
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Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
backgroundMicroarrays for the analysis of gene expression are of three different types: short oligonucleotide (25-30 base), long oligonucleotide (50-80 base), and cDNA (highly variable in length). The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date, but long oligonucleotide platforms are gaining in popularity and will probably replace cDNA arrays. As part of a validation study for the long oligonucleotide arrays, we compared and contrasted expression profiles from the three formats, testing RNA from six different cell lines against a universal reference standard.
resultsThe three platforms had 6430 genes in common. In general, correlation of gene expression levels across the platforms was good when defined by concordance in the direction of expression difference (upregulation or downregulation), scatter plot analysis, principal component analysis, cell line correlation or quantitative RT-PCR. The overall correlations (r values) between platforms were in the range 0.7 to 0.8, as determined by analysis of scatter plots. When concordance was measured for expression ratios significant at p-values of <0.05 and at expression threshold levels of 1.5 and 2-fold, the agreement among the platforms was very high, ranging from 93% to 100%.
conclusionOur results indicate that the long oligonucleotide platform is highly suitable for expression analysis and compares favorably with the cDNA and short oligonucleotide varieties. All three platforms can give similar and reproducible results if the criterion is the direction of change in gene expression and minimal emphasis is placed on the magnitude of change.
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