ArticleBMC genomics2003
Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance.
Article in BMC genomics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Nutritional Status and Associated Risk Factors of Syrian Children's Residents in the Kingdom of Saudi Arabia.Children (Basel, Switzerland) · 2021Article
- Power in pairs: assessing the statistical value of paired samples in tests for differential expression.BMC genomics · 2018Article
- Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota.Frontiers in microbiology · 2018Article
- Impact of blood collection and processing on peripheral blood gene expression profiling in type 1 diabetes.BMC genomics · 2017Article
- Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq.BMC biotechnology · 2015Article
- The stage-specific testicular germ cell apoptotic response to low-dose X-irradiation and 2,5-hexanedione combined exposure. I: Validation of the laser capture microdissection method for qRT-PCR array application.Toxicologic pathology · 2014Article
- Cross-species hybridization of microarrays for studying tumor transcriptome of brain metastasis.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Spatio-temporal regulation of Wnt and retinoic acid signaling by tbx16/spadetail during zebrafish mesoderm differentiation.BMC genomics · 2010Article
- Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling.BMC genomics · 2009Article
- Sub-telomere directed gene expression during initiation of invasive aspergillosis.PLoS pathogens · 2008Article
- Article
- Single molecule transcription profiling with AFM.Nanotechnology · 2007Article
- Evaluation of global RNA amplification and its use for high-throughput transcript analysis of laser-microdissected endosperm.International journal of plant genomics · 2007Article
- Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling.Nucleic acids research · 2006Review
- Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level.Genome biology · 2006Article
- Limitations of mRNA amplification from small-size cell samples.BMC genomics · 2005Article
- Expression profiling of gastric cancer samples by oligonucleotide microarray analysis reveals low degree of intra-tumor variability.World journal of gastroenterology · 2005Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA limiting factor of cDNA microarray technology is the need for a substantial amount of RNA per labeling reaction. Thus, 20-200 micro-grams total RNA or 0.5-2 micro-grams poly (A) RNA is typically required for monitoring gene expression. In addition, gene expression profiles from large, heterogeneous cell populations provide complex patterns from which biological data for the target cells may be difficult to extract. In this study, we chose to investigate a widely used mRNA amplification protocol that allows gene expression studies to be performed on samples with limited starting material. We present a quantitative study of the variation and noise present in our data set obtained from experiments with either amplified or non-amplified material.
resultsUsing analysis of variance (ANOVA) and multiple hypothesis testing, we estimated the impact of amplification on the preservation of gene expression ratios. Both methods showed that the gene expression ratios were not completely preserved between amplified and non-amplified material. We also compared the expression ratios between the two cell lines for the amplified material with expression ratios between the two cell lines for the non-amplified material for each gene. With the aid of multiple t-testing with a false discovery rate of 5%, we found that 10% of the genes investigated showed significantly different expression ratios.
conclusionAlthough the ratios were not fully preserved, amplification may prove to be extremely useful with respect to characterizing low expressing genes.
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