COMODO

COMODO identifies conserved coexpression modules between species by analyzing microarray expression compendia together with gene homology maps to detect module pairs with statistically significant shared homologs.

Key Features:

• Objective Selection Criterion: Employs an objective selection criterion to identify conserved module pairs based on the number of shared homologs relative to module size.
• Input Data: Uses microarray expression data and a gene homology map as inputs for cross-species analysis.
• Module Identification: Identifies coexpression modules within each species' expression compendium.
• Cross-Species Comparison: Compares modules across species to detect pairs with significant overlap in homologous genes.
• Output: Produces pairs of conserved modules prioritized by the statistical significance of shared homologs.
• Statistical Significance Assessment: Assesses significance of module pair overlap relative to module size to prioritize biologically meaningful conservation.

Scientific Applications:

• Comparative Genomics: Identifies conserved coexpression modules to infer biological processes preserved across species.
• Evolutionary Biology: Enables analysis of evolutionary conservation of gene coexpression and regulatory networks.
• Microbial Comparative Transcriptomics: Applied to compare coexpression conservation between Escherichia coli and Bacillus subtilis.

Methodology:

Uses microarray expression data and a gene homology map as inputs.
Identifies coexpression modules within each species' dataset.
Compares modules across species to find pairs with significant overlap in shared homologs.
Assesses statistical significance of module pair overlap relative to module size.