GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana

Circadian rhythms regulate crucial physiological processes in plants, making the analysis of rhythmic gene expression vital for understanding how plants adapt to and anticipate daily environmental changes, and for improving agricultural traits. Foundational databases for plant circadian rhythms have been invaluable, but face challenges in keeping pace with the rapid accumulation of modern transcriptomic data, particularly for the most widely used model organism, Arabidopsis thaliana. To address this critical gap, we developed GEAR (Gene Expression Archives for Rhythm), a new database resource dedicated to A. thaliana that serves as an integrated atlas of gene expression dynamics. GEAR builds a comprehensive data archive by integrating both legacy microarray and modern RNA-seq datasets, covering 83 diverse experimental conditions. Its intuitive web interface functions as an interactive atlas, allowing users to compare expression profiles not only across different experimental treatments but also across independent studies conducted under nominally identical settings. This unique feature enables researchers to move beyond single-experiment findings and distinguish robust biological signals from interlaboratory variability. For the first time, this allows for a meta-analysis to define a high-confidence set of core clock-regulated genes, providing foundational insights into the most conserved outputs of the plant circadian network.