CEMiTool

CEMiTool identifies and analyzes coexpression gene modules in transcriptomic datasets to elucidate systems-level gene functionality.

Key Features:

• Automated module discovery and analysis: Detects coexpression gene modules through modular gene co-expression network analysis.
• Pathway enrichment and sample-group alteration evaluation: Tests modules for pathway over-representation and evaluates module activity or alterations across defined sample groups.
• Interactome integration and hub identification: Integrates transcriptomic data with interactome information to pinpoint potential network hubs within modules.
• Bioconductor implementation and transcriptomic support: Implemented as a Bioconductor package and applicable to transcriptomic data including RNA-seq.

Scientific Applications:

• Large-scale transcriptome analysis: Applied to over 1,000 transcriptome datasets to assess module structure across diverse biological contexts.
• Infectious disease transcriptomics (Leishmania): Analyzed an RNA-seq dataset from patients infected with Leishmania to reveal module-level insights into disease physiopathology.

Methodology:

Automated construction of gene co-expression networks and module detection, followed by pathway enrichment analysis, evaluation of module alterations across sample groups, and integration with interactome data to identify potential network hubs.