GeneCodis3

GeneCodis3 performs integrative functional enrichment and modular analysis of gene lists to identify enriched annotations and coherent gene modules by combining diverse biological information.

Key Features:

• Modular Enrichment Analysis: Identifies modular patterns of interrelated annotations to discover functionally coherent gene modules.
• Enrichment Analysis: Performs traditional singular enrichment analysis and supports comparative/differential analysis across gene sets.
• Regulatory Patterns and User-Defined Annotations: Incorporates regulatory pattern annotations and accepts user-defined custom annotations.
• Noise Reduction and Data Summarization: Implements an algorithm that reduces noisy and redundant enrichment results and summarizes enriched terms into modules.
• Expanded Biological Information Sources: Integrates additional sources including genetic diseases, drug-gene interactions, and PubMed-derived information.
• SOAP Web Services: Exposes a public SOAP web services interface for programmatic integration into scripts and workflows.
• Performance and Scalability: Re-engineered for improved computational performance and scalability.

Scientific Applications:

• Gene expression profiling: Interpretation of gene expression profiling results through enrichment and module detection.
• Genome-wide association studies (GWAS): Functional annotation and module discovery for GWAS-derived gene lists.
• High-throughput experiments: Functional analysis of gene lists from diverse high-throughput techniques.
• Studies of genetic diseases, drug-gene interactions, and regulatory networks: Integration of disease, drug-interaction, and PubMed annotations to explore genetic disease mechanisms, drug-gene relationships, and regulatory networks.

Methodology:

Combines multiple annotation sources to perform singular and modular enrichment analyses, identifies enriched terms, aggregates them into gene modules, and applies an algorithm to reduce noise and redundancy.