ArticleGenome biology2002
Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments.
Article in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 2 of them syntheses that pooled it.
What it found
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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
86 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Demasculinization of the Anopheles gambiae X chromosome.BMC evolutionary biology · 2012Pooled it
- Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics.Ecotoxicology (London, England) · 2011Pooled it
- Light sensing by opsins and fungal ecology: NOP-1 modulates entry into sexual reproduction in response to environmental cues.Molecular ecology · 2018Article
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- Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection.Molecular biology and evolution · 2015Article
- Variation in the X:Autosome Distribution of Male-Biased Genes among Drosophila melanogaster Tissues and Its Relationship with Dosage Compensation.Genome biology and evolution · 2015Article
- Social odors conveying dominance and reproductive information induce rapid physiological and neuromolecular changes in a cichlid fish.BMC genomics · 2015Article
- Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola.PloS one · 2015Article
- Cautions about the reliability of pairwise gene correlations based on expression data.Frontiers in microbiology · 2015Article
- Identification of differentially-expressed genes in intestinal gastric cancer by microarray analysis.Genomics, proteomics & bioinformatics · 2014Article
- Interaction between bisphenol A and dietary sugar affects global gene transcription in Drosophila melanogaster.Genomics data · 2014Article
- Epigenetic inheritance and genome regulation: is DNA methylation linked to ploidy in haplodiploid insects?Proceedings. Biological sciences · 2014Article
- The TAF9 C-terminal conserved region domain is required for SAGA and TFIID promoter occupancy to promote transcriptional activation.Molecular and cellular biology · 2014Article
- High intake of dietary sugar enhances bisphenol A (BPA) disruption and reveals ribosome-mediated pathways of toxicity.Genetics · 2014Article
- Genome-wide gene expression effects of sex chromosome imprinting in Drosophila.G3 (Bethesda, Md.) · 2014Article
- Passage through the mammalian gut triggers a phenotypic switch that promotes Candida albicans commensalism.Nature genetics · 2013Article
- Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma.Proceedings. Biological sciences · 2013Article
- Chromatin-associated proteins HP1 and Mod(mdg4) modify Y-linked regulatory variation in the drosophila testis.Genetics · 2013Article
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26 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
2 authors.
Funding
Abstract
backgroundMethods of microarray analysis that suit experimentalists using the technology are vital. Many methodologies discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly applied to multifactorial experimental design. Here we present a flexible, quantitative Bayesian framework. This framework can be used to analyze normalized microarray data acquired by any replicated experimental design in which any number of treatments, genotypes, or developmental states are studied using a continuous chain of comparisons.
resultsWe apply this method to Saccharomyces cerevisiae microarray datasets on the transcriptional response to ethanol shock, to SNF2 and SWI1 deletion in rich and minimal media, and to wild-type and zap1 expression in media with high, medium, and low levels of zinc. The method is highly robust to missing data, and yields estimates of the magnitude of expression differences and experimental error variances on a per-gene basis. It reveals genes of interest that are differentially expressed at below the twofold level, genes with high 'fold-change' that are not statistically significantly different, and genes differentially regulated in quantitatively unanticipated ways.
conclusionsAnyone with replicated normalized cDNA microarray ratio datasets can use the freely available MacOS and Windows software, which yields increased biological insight by taking advantage of replication to discern important changes in expression level both above and below a twofold threshold. Not only does the method have utility at the moment, but also, within the Bayesian framework, there will be considerable opportunity for future development.
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Registered trials
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.