TFLink

TFLink aggregates and harmonizes approximately 12 million transcription factor-target gene interactions and around 9 million nucleotide sequences and genomic locations of transcription factor binding sites across human and six model organisms (mouse, rat, zebrafish, fruit fly, worm, and yeast) to support comparative and regulatory genomics.

Key Features:

• Data scope: Approximately 12 million transcription factor-target gene interactions and around 9 million nucleotide sequences and genomic locations of transcription factor binding sites covering human, mouse, rat, zebrafish, fruit fly, worm, and yeast.
• Integration of multiple resources: Aggregates and integrates data from ten distinct external resources to produce a comprehensive dataset.
• Experimental validation annotation: Entries are curated and labeled with the type and volume of experiments, ranging from small-scale studies to high-throughput analyses.
• Standardized data formats: Regulatory data are standardized and provided for download in multiple formats.
• Cross-species comparability: Data across multiple species enable comparative studies of gene regulation and the evolution of signal transduction pathways.

Scientific Applications:

• Functional Genomics: Exploration of transcriptional regulatory interactions to investigate gene function and regulation.
• Systems Biology: Analysis of large-scale regulatory networks and interactions for systems-level modeling.
• Comparative Gene Regulation Studies: Cross-species comparisons of regulatory interactions to study conservation and divergence of regulatory mechanisms.
• Gene Set Enrichment Analyses: Use of curated transcription factor-target gene sets for enrichment analyses and interpretation of experimental results.

Methodology:

Aggregates data from ten external resources, curates entries with annotation of experimental type and scale (small-scale to high-throughput), and standardizes regulatory data while providing nucleotide sequences and genomic locations of transcription factor binding sites.