GeneCAT

GeneCAT performs multigene co-expression analysis and ortholog identification on microarray-derived gene expression data to infer gene function and regulatory networks in plants.

Key Features:

• Multigene co-expression analysis: Extends single-gene analysis to multigene co-expression and co-expressed gene networks to identify complex gene interactions and regulatory modules in plant genomes.
• Map-O-Matic: Matches co-expression patterns of multiple query genes against a user-defined subdatabase to support mapping genes based on expression profiles, including use in forward genetic screens.
• Rosetta integration with BLAST: Combines co-expression analysis with BLAST sequence alignment to assist identification of 'true' gene orthologs and enhance cross-species functional inference for organisms such as Arabidopsis thaliana and Hordeum vulgare (Barley).

Scientific Applications:

• Arabidopsis thaliana expression analysis: Mining microarray expression data to elucidate gene function and regulatory networks in the model plant Arabidopsis thaliana.
• Hordeum vulgare (Barley) co-expression mining: Extending co-expression analyses and network mining to the monocot Barley for comparative and functional studies.
• Forward genetic screens and gene mapping: Using co-expression pattern matching to support mapping of genes identified in forward genetic screens.
• Cross-species functional inference and evolutionary studies: Integrating co-expression patterns with sequence similarity to predict orthologs and inform evolutionary and functional genomics analyses.

Methodology:

Performs microarray-based co-expression analysis using multigene co-expression and network-based approaches, matches co-expression patterns against user-defined subdatabases (Map-O-Matic), and integrates BLAST sequence alignment (Rosetta) for ortholog identification.