TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Times-Series Data in CircadianBiology Research

BioRxiv : the Preprint Server for Biology
E. Ness-CohnRosemary Braun

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 (https://github.com/nesscoder/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. By supplying a tool to vary and optimize these considerations, TimeTrial will enhance circadian transcriptomics studies.

Related Concepts

Response to Cold
Environment
Electron Transport
Shock
Chlorophyll Fluorescence
Clone
Tissue Culture Techniques
Laboratory Culture
Attention
Norwegians

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

Computer Methods in Biomechanics and Biomedical Engineering
F BeaumontF Grappe
International Journal of Sports Medicine
G Watson, T Swensen
International Journal of Sport Nutrition and Exercise Metabolism
Thomas M DoeringCecilia M Shing
© 2020 Meta ULC. All rights reserved