GeneCodis

GeneCodis performs functional enrichment and ontological analyses to identify statistically significant concurrent annotations in lists of genes, proteins, and regulatory elements (miRNAs, transcription factors, CpG sites) for interpreting biological mechanisms.

Key Features:

• Functional enrichment analysis: Performs functional enrichment analysis to detect overrepresented biological terms and categories in input lists.
• Ontological analyses: Conducts ontological analyses to map input entities to controlled vocabularies and ontology terms.
• Supported input entities: Analyzes lists of genes, proteins, miRNAs, transcription factors, and CpG sites.
• Integration of annotation databases: Integrates multiple sources of annotations and annotation databases for comprehensive mapping.
• Statistical scoring of enrichment: Assigns statistical scores to evaluate the significance of enriched annotations.
• Identification of concurrent annotations: Identifies statistically significant concurrent annotations within input gene lists.
• Expanded regulatory element support (GeneCodis 4): Extends functional analysis to include regulatory elements alongside traditional gene and protein data.

Scientific Applications:

• Interpretation of biological mechanisms: Enables interpretation of underlying biological mechanisms by linking input entities to enriched annotations.
• Pathway and process analysis: Facilitates characterization of biological processes and pathways associated with gene and regulatory element lists.
• Gene function and regulatory mechanism discovery: Supports discovery of gene functions and regulatory mechanisms through combined annotation enrichment.
• Genomic research analyses: Applies to diverse genomic research contexts that require annotation-driven interpretation of gene- or regulator-centric datasets.

Methodology:

Integration of multiple annotation databases combined with statistical scoring to evaluate enrichment significance and identification of statistically significant concurrent annotations.