CAST-R

CAST-R identifies and visualizes circadian and heat stress-responsive gene expression and regulatory interactions across plant species including Arabidopsis thaliana, Brassica rapa, Hordeum vulgare (barley), and Oryza sativa (rice) to support study of temporal gene regulation under environmental stimuli.

Key Features:

• Gene Visualization: Generates and exports transcript abundance profiles and heatmaps across a 24-hour cycle, including responses to heat stress and recovery phases for specified Arabidopsis thaliana genes.
• Interactive Network Analysis: Visualizes networks connecting clock proteins and target genes using published chromatin immunoprecipitation-sequencing (ChIP-seq) datasets from Arabidopsis.
• Phase Enrichment Analyses: Performs statistical phase enrichment analyses on rhythmic gene expression datasets across species to identify significantly over- or underrepresented phases within gene subsets.
• Cross-Species Data Integration: Supports visualization of circadian transcript abundance datasets from Arabidopsis thaliana, Brassica rapa, Hordeum vulgare (barley), and Oryza sativa (rice) for comparative analyses.

Scientific Applications:

• Circadian regulation studies: Characterizing temporal patterns of gene expression and clock-controlled regulation in plants.
• Heat stress response analysis: Identifying genes responsive to heat stress and profiling recovery dynamics over diel cycles.
• Comparative and translational research: Comparing circadian transcriptomes across Arabidopsis, Brassica rapa, Hordeum vulgare, and Oryza sativa to inform crop resilience and breeding efforts.

Methodology:

Generates transcript abundance profiles and heatmaps across 24-hour time courses; uses published chromatin immunoprecipitation-sequencing (ChIP-seq) datasets to construct protein–target interaction networks; performs statistical phase enrichment analyses on rhythmic gene expression datasets and integrates circadian transcriptomic datasets across listed plant species.