metaRE

metaRE identifies cis-regulatory elements by meta-analysis of transcriptomic datasets (microarray and RNA-Seq) to detect promoter motifs associated with differential gene expression across multiple experiments.

Key Features:

• Systematic search for cis-regulatory elements: Systematically searches for cis-regulatory elements enriched in gene promoters that exhibit significant transcriptional changes.
• Integration of multiple datasets: Integrates multiple expression profiling datasets (microarray and RNA-Seq) from the same organism responding to diverse stimuli.
• Identification of simple and composite elements: Identifies both simple and composite cis-regulatory elements systematically associated with differential gene expression.
• Performance demonstration: Has been applied to identify cold stress-responsive cis-regulatory codes in Arabidopsis thaliana.
• Discovery of known and unknown regulators: Detects motifs corresponding to known regulators and uncovers associations with previously unknown regulatory elements involved in specific responses.

Scientific Applications:

• Transcriptional reprogramming studies: Analyzes transcriptional changes to elucidate molecular mechanisms underlying physiological and morphological adaptations.
• Complex pathway analysis: Dissects cis-regulatory codes in complex responses where multiple signaling pathways are active, such as temperature changes, dehydration, and exposure to biologically active substances.

Methodology:

Performs a meta-analytical integration of expression profiling experiments, focuses on promoters of genes with significantly altered transcription levels, and identifies enriched cis-regulatory elements.