famat

Famat collects and integrates functional data about user-provided gene and metabolite lists, enabling pathway enrichment analysis, Gene Ontology enrichment analysis, and interactive visualization of molecular relationships and pathway hierarchies.

Key Features:

• Pathway Enrichment Analysis: Identifies pathways containing user-provided genes and metabolites.
• Direct Interaction Mapping: Detects direct interactions between user elements inside pathways.
• Element Annotation: Retrieves identifiers and descriptions for genes and metabolites.
• Gene Ontology Enrichment Analysis: Performs GO term enrichment on user genes using Molecular Function and Biological Process categories.
• Pathway Hierarchy Heatmap: Generates a heatmap showing which elements from the list are present in pathways structured in hierarchies.
• GO Term Hierarchy Visualization: Displays hierarchies of enriched GO terms.

Scientific Applications:

• Integrated Omics Analysis: Combines metabolic and transcriptomic data for joint functional interpretation.
• Pathway-Centric Data Exploration: Identifies relevant biological pathways and molecular interactions from gene and metabolite lists.
• Functional Annotation: Characterizes gene sets through GO term enrichment and pathway mapping.

Methodology:

Pathway enrichment analysis is performed to identify pathways containing user genes and metabolites; Gene Ontology enrichment analysis is performed on user genes using Molecular Function and Biological Process categories.