HTRgene

HTRgene identifies "response order preserving differentially expressed genes" (DEGs) by integrating multiple heterogeneous time-series gene expression datasets collected under uniform stress conditions to detect genes that maintain consistent response order across samples.

Key Features:

• Integrated time-series analysis: Integrates multiple heterogeneous time-series gene expression datasets where stress strength and number of time points can vary across samples.
• Response order preserving DEGs: Identifies "response order preserving differentially expressed genes" (DEGs) that exhibit differential expression while maintaining a consistent response order across datasets.
• Ordering-based detection: Focuses on the ordering of gene response times across samples to improve detection of stress-response genes.
• Validation on Arabidopsis: Validated using 28 and 24 time-series samples from Arabidopsis subjected to cold and heat stress, respectively.
• Reproduction of known responses: Reproduced documented biological responses associated with cold and heat stress in Arabidopsis.
• Comparative accuracy: Demonstrated superior accuracy compared to existing tools in identifying documented stress-response genes.
• Improved biological inference: Enables uncovering biological mechanisms with higher precision through integrated analysis of heterogeneous time-series data.

Scientific Applications:

• Stress-response gene discovery: Detection of genes involved in stress responses that preserve response order across multiple time-series datasets.
• Comparative stress analysis: Comparative analysis of cold versus heat stress responses in Arabidopsis using time-series expression data.
• Cross-sample integration: Integration of datasets with varying time points and stress intensities to identify conserved temporal response patterns.
• Method benchmarking and validation: Benchmarking and validation of documented stress-response gene sets by comparison to existing methods.

Methodology:

Integrates and analyzes heterogeneous time-series gene expression datasets and identifies response order preserving DEGs by assessing consistent response ordering across samples; validated on 28 cold and 24 heat stress Arabidopsis time-series and compared to existing tools.