ArticleNucleic acids research2008
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 414 papers, 2 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
414 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The miRNA Mirage: How Close Are We to Finding a Non-Invasive Diagnostic Biomarker in Endometriosis? A Systematic Review.International journal of molecular sciences · 2018Pooled it
- High expression of SMARCA4 or SMARCA2 is frequently associated with an opposite prognosis in cancer.Scientific reports · 2018Pooled it
- MicroRNome analysis generates a blood-based signature for endometriosis.Scientific reports · 2022Trial
- Gene-expression and in vitro function of mesenchymal stromal cells are affected in juvenile myelomonocytic leukemia.Haematologica · 2015Trial
- Small RNA sequencing revealed microRNAs involved in growth and development of the oyster mushroom Pleurotus ostreatus.Antonie van Leeuwenhoek · 2026Article
- A Distinct Defense Strategy: The Molecular Basis of WSSV Tolerance inInternational journal of molecular sciences · 2026Article
- Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications.Bioengineering (Basel, Switzerland) · 2025Review
- Analysis of the miRNA Transcriptome inInternational journal of molecular sciences · 2025Article
- Effects and mechanisms of glyphosate as phosphorus nutrient on element stoichiometry and metabolism in the diatomApplied and environmental microbiology · 2024Article
- EnhancingFrontiers in plant science · 2024Article
- Enabling biomedical technologies for chronic myelogenous leukemia (CML) biomarkers detection.Biomicrofluidics · 2024Review
- Combination of RCA and DNAzyme for Dual-Signal Isothermal Amplification of Exosome RNA.Molecules (Basel, Switzerland) · 2023Article
- Comparative Transcriptome Profiling Reveals Key MicroRNAs and Regulatory Mechanisms for Aluminum Tolerance in Olive.Plants (Basel, Switzerland) · 2023Article
- Characterizations of microRNAs involved in the molecular mechanisms underlying the therapeutic effects of noni (Frontiers in nutrition · 2023Article
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- Preparation and processing of dried blood spots for microRNA sequencing.Biology methods & protocols · 2023Review
- MicroRNA-like RNA Functions Are Required for the Biosynthesis of Active Compounds in the Medicinal FungusMicrobiology spectrum · 2022Article
- A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding.Cell research · 2022Article
- Vasorin Deletion in C57BL/6J Mice Induces Hepatocyte Autophagy through Glycogen-Mediated mTOR Regulation.Nutrients · 2022Article
354 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The hippocampal expression profiles of wild-type mice and mice transgenic for deltaC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray platforms. With Illumina's digital gene expression assay, we obtained approximately 2.4 million sequence tags per sample, their abundance spanning four orders of magnitude. Results were highly reproducible, even across laboratories. With a dedicated Bayesian model, we found differential expression of 3179 transcripts with an estimated false-discovery rate of 8.5%. This is a much higher figure than found for microarrays. The overlap in differentially expressed transcripts found with deep sequencing and microarrays was most significant for Affymetrix. The changes in expression observed by deep sequencing were larger than observed by microarrays or quantitative PCR. Relevant processes such as calmodulin-dependent protein kinase activity and vesicle transport along microtubules were found affected by deep sequencing but not by microarrays. While undetectable by microarrays, antisense transcription was found for 51% of all genes and alternative polyadenylation for 47%. We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.