WebGestalt

WebGestalt performs functional enrichment and gene-set analyses to identify enriched biological categories and contextual annotations for large-scale gene lists.

Key Features:

• Gene set operations: Supports Boolean unions, intersections, and differences between gene sets for comparative analyses.
• Attribute retrieval: Retrieves up to 20 attributes per gene from diverse databases, accepts multiple gene identifiers across eight supported organisms, and accommodates data from genetic, transcriptomic, and proteomic platforms.
• Contextual annotation and visualization: Organizes and visualizes gene sets across Gene Ontology, tissue expression patterns, chromosomal distribution, metabolic pathways, signaling pathways, protein domain information, and publications.
• Statistical enrichment: Recommends and performs statistical tests to identify significant biological areas within gene sets.
• Functional enrichment coverage: Performs enrichment analysis across 78,612 categories from curated databases and computational analyses, including Gene Ontology terms, pathways, network modules, gene-phenotype, gene-disease, gene-drug associations, and chromosomal locations.
• Visualization modalities: Generates pathway maps, hierarchical network visualizations, and phenotype ontology visualizations for interpretation of enrichment results.

Scientific Applications:

• Gene expression analysis: Applied to analyze gene expression data derived from high-throughput technologies.
• Tissue-specific gene set exploration: Used to explore 48 human tissue-specific gene sets and identify over-represented genes across tissues.
• Type 2 diabetes mellitus research: Employed to identify key transcription factors and pathways involved in T2DM pathogenesis.

Methodology:

Retrieves up to 20 attributes per gene from multiple databases, supports multiple gene identifiers across eight organisms, performs Boolean set operations, applies statistical tests for enrichment, conducts functional enrichment across 78,612 categories, and generates pathway maps, hierarchical network and phenotype ontology visualizations.