CARRIE

CARRIE infers transcriptional regulatory networks from microarray expression data and promoter sequences to elucidate how specific stimuli influence gene expression.

Key Features:

• Interactive Network Visualization: Provides interactive graph-based visualizations of inferred transcriptional regulatory networks.
• Integration with KEGG XML (KGML): Supports inclusion of network data in KEGG XML (KGML) format to facilitate integration with other bioinformatics tools and databases.
• Gene Ontology Annotation: Annotates genes with Gene Ontology terms to support functional interpretation of network components.

Scientific Applications:

• Systems Biology and Functional Genomics: Reconstructing transcriptional regulatory networks in response to specific stimuli for systems-level and functional genomics investigations.
• Hypothesis Generation: Generating hypotheses about gene function and regulatory relationships in contexts such as disease states or developmental processes.
• Candidate Identification: Identifying candidate transcription factors, target genes, and pathways involved in cellular responses.

Methodology:

Analyzes microarray expression data together with promoter sequence information to construct putative transcriptional regulatory networks, identify key transcription factors, and map their target genes.