FuncTree

FuncTree maps high-throughput genomic, metagenomic, and transcriptomic data onto a hierarchical functional representation derived from the KEGG database to visualize functional landscapes and detect statistically enriched functions.

Key Features:

• Functional Tree Map Visualization: Maps user-provided omics data onto a predefined circular dendrogram that encodes hierarchical relationships among biological functions cataloged in the KEGG database.
• Customizable analysis parameters and statistical enrichment: Implements calculation methods to identify statistically enriched functions by comparing omics datasets against predefined reference datasets.
• Validation on diverse datasets: Applied to pan-genomic data from three bacterial genera, metagenomic data from the human gut, and transcriptomic data from two types of human cell expression to validate functional representation and enrichment detection.

Scientific Applications:

• Genomic and pan-genomic analysis: Mapping genomic and pan-genomic data to KEGG hierarchical functions to characterize functional repertoires of organisms.
• Metagenomics studies: Assessing microbial community functional potential in human gut metagenomic datasets using KEGG-based functional hierarchies.
• Transcriptomics analysis: Interpreting gene expression from two types of human cell expression to elucidate functional changes and cellular responses.

Methodology:

Maps omics data onto a predefined circular dendrogram that integrates hierarchical function relationships from the KEGG database and performs statistical enrichment analysis by comparing datasets to predefined references using internal calculation methods.