ArticleBMC genomics2009
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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92 citing papers in PubMed.
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- Multifaceted Stoichiometry Control of Bacterial Operons Revealed by Deep Proteome Quantification.Frontiers in genetics · 2019Article
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- Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma.Journal of experimental & clinical cancer research : CR · 2018Article
- Modeling and analysis of RNA-seq data: a review from a statistical perspective.Quantitative biology (Beijing, China) · 2018Article
- Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.).Biological research · 2018Article
- TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.Nucleic acids research · 2018Article
- Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2018Article
- TISSUES 2.0: an integrative web resource on mammalian tissue expression.Database : the journal of biological databases and curation · 2018Article
- Proteogenomics in Aid of Host-Pathogen Interaction Studies: A Bacterial Perspective.Proteomes · 2017Review
32 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
backgroundHigh-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.
resultsConsequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae.
conclusionUsing a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.
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