TFTenricher

TFTenricher performs annotation enrichment analysis of genes targeted by user-defined sets of human transcription factors to identify over-represented Gene Ontology terms, KEGG and Reactome pathways, and disease associations among downstream TF targets.

Key Features:

• Targeted Enrichment Analysis: Identifies over-represented Gene Ontology (GO) terms, KEGG pathways, Reactome pathways, and disease associations among downstream target genes of transcription factors.
• Co-expression-based Inference: Evaluates downstream gene targets using co-expression data to infer TF target sets and predict downstream processes with minimal false positive annotations.
• Integration with Major Databases: Performs functional enrichment using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome.
• Demonstrated Disease Application: Applied to differential expression of TFs across 21 diseases to identify significant disease-related terms beyond transcription-centric processes.

Scientific Applications:

• Pathway and Process Exploration: Characterizes biological pathways and downstream processes influenced by transcription factors through enrichment of inferred TF target genes.
• Disease Mechanism Identification: Reveals disease-related functional terms from differential TF expression analyses across multiple disease datasets (21 diseases).

Methodology:

Infers downstream TF targets using co-expression data and performs over-representation/enrichment analysis of those targets using Gene Ontology (GO), KEGG, and Reactome annotations.