SynthesisPLoS computational biology2007
Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes.
Synthesis in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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
65 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses.Journal of biological rhythms · 2023Pooled it
- Guidelines for Genome-Scale Analysis of Biological Rhythms.Journal of biological rhythms · 2017Guideline
- Molecular correlates of sleep deprivation in the mouse brain identified by meta-analysis of microarray data.Neurobiology of sleep and circadian rhythms · 2026Article
- Early photoperiodic cues modulate capacity for adult cold tolerance in the yellow fever mosquito Aedes aegypti.The Journal of experimental biology · 2026Article
- A curated tissue-specific proteome, phosphoproteome, and kinome map of Drosophila melanogaster with an integrated outlook in circadian physiology.Functional & integrative genomics · 2025Article
- Uncovering the circadian transcriptome ofProceedings. Biological sciences · 2024Article
- A plant cytorhabdovirus modulates locomotor activity of insect vectors to enhance virus transmission.Nature communications · 2023Article
- Roles of peripheral clocks: lessons from the fly.FEBS letters · 2022Review
- Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Identification of Genes Contributing to a Long Circadian Period inJournal of biological rhythms · 2021Article
- Loss of function in the Drosophila clock gene period results in altered intermediary lipid metabolism and increased susceptibility to starvation.Cellular and molecular life sciences : CMLS · 2020Article
- Molecular mechanisms and physiological importance of circadian rhythms.Nature reviews. Molecular cell biology · 2020Review
- Daily Variations in the Expression of Genes Related to Insecticide Resistance in the Chagas Disease VectorThe American journal of tropical medicine and hygiene · 2019Article
- Metabolic oscillations on the circadian time scale inMolecular systems biology · 2018Article
- Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data.Journal of biological rhythms · 2018Article
- Circadian regulation of metabolism and healthspan in Drosophila.Free radical biology & medicine · 2018Review
- Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism PlantFrontiers in plant science · 2018Article
- Circadian Plasticity in the Brain of Insects and Rodents.Frontiers in neural circuits · 2018Review
- Improving Reproducibility and Candidate Selection in Transcriptomics Using Meta-analysis.Journal of experimental neuroscience · 2018Article
- Regulation of circadian clock transcriptional output by CLOCK:BMAL1.PLoS genetics · 2018Article
5 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Five independent groups have reported microarray studies that identify dozens of rhythmically expressed genes in the fruit fly Drosophila melanogaster. Limited overlap among the lists of discovered genes makes it difficult to determine which, if any, exhibit truly rhythmic patterns of expression. We reanalyzed data from all five reports and found two sources for the observed discrepancies, the use of different expression pattern detection algorithms and underlying variation among the datasets. To improve upon the methods originally employed, we developed a new analysis that involves compilation of all existing data, application of identical transformation and standardization procedures followed by ANOVA-based statistical prescreening, and three separate classes of post hoc analysis: cross-correlation to various cycling waveforms, autocorrelation, and a previously described fast Fourier transform-based technique. Permutation-based statistical tests were used to derive significance measures for all post hoc tests. We find application of our method, most significantly the ANOVA prescreening procedure, significantly reduces the false discovery rate relative to that observed among the results of the original five reports while maintaining desirable statistical power. We identify a set of 81 cycling transcripts previously found in one or more of the original reports as well as a novel set of 133 transcripts not found in any of the original studies. We introduce a novel analysis method that compensates for variability observed among the original five Drosophila circadian array reports. Based on the statistical fidelity of our meta-analysis results, and the results of our initial validation experiments (quantitative RT-PCR), we predict many of our newly found genes to be bona fide cyclers, and suggest that they may lead to new insights into the pathways through which clock mechanisms regulate behavioral rhythms.
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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.