ArticleJournal of biological rhythms2020
TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research.
Article in Journal of biological rhythms, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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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
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses.Journal of biological rhythms · 2023Pooled it
- Article
- Detecting Rhythmic Gene Expression in Single-cell Transcriptomics.Journal of biological rhythms · 2024Article
- Detecting Rhythmic Gene Expression in Single Cell Transcriptomics.bioRxiv : the preprint server for biology · 2024Article
- Temperature-driven coordination of circadian transcriptional regulation.PLoS computational biology · 2024Article
- Circadian gene transcription plays a role in cellular metabolism in hibernating brown bears, Ursus arctos.Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · 2023Article
- Temperature-driven coordination of circadian transcriptome regulation.bioRxiv : the preprint server for biology · 2023Article
- Experimental design and power calculation in omics circadian rhythmicity detection using the cosinor model.Statistics in medicine · 2023Article
- Integrative Analysis of Rhythmicity: From Biology to Urban Environments and Sustainability.International journal of environmental research and public health · 2022Review
- Roles of peripheral clocks: lessons from the fly.FEBS letters · 2022Review
- RhythmicDB: A Database of Predicted Multi-Frequency Rhythmic Transcripts.Frontiers in genetics · 2022Article
- Comment on "Circadian rhythms in the absence of the clock geneScience (New York, N.Y.) · 2021Article
- Daily transcriptomes of the copepod Calanus finmarchicus during the summer solstice at high Arctic latitudes.Scientific data · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues, coordinating physiological processes. The effect of this rhythm on health has generated increasing interest in discovering genes under circadian control by searching for periodic patterns in transcriptomic time-series experiments. While algorithms for detecting cycling transcripts have advanced, there remains little guidance quantifying the effect of experimental design and analysis choices on cycling detection accuracy. We present TimeTrial, a user-friendly benchmarking framework using both real and synthetic data to investigate cycle detection algorithms' performance and improve circadian experimental design. Results show that the optimal choice of analysis method depends on the sampling scheme, noise level, and shape of the waveform of interest and provides guidance on the impact of sampling frequency and duration on cycling detection accuracy. The TimeTrial software is freely available for download and may also be accessed through a web interface. By supplying a tool to vary and optimize experimental design considerations, TimeTrial will enhance circadian transcriptomics 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.