TFutils

TFutils provides harmonized catalogs and utility functions to integrate transcription factor (TF) annotations from CISBP, HOCOMOCO, Gene Ontology, MSigDb, and ENCODE with genomic and transcriptomic datasets for analysis of gene regulatory mechanisms.

Key Features:

• Harmonized TF catalogs: Provides reconciled human transcription factor listings from CISBP, HOCOMOCO, and Gene Ontology.
• TF–target catalog: Supplies a curated TF–target catalog derived from MSigDb.
• ENCODE TF binding data access: Offers programmatic access to results from 690 ENCODE TF binding experiments.
• TF binding site identification: Supports multiple approaches for identifying TF binding sites.
• Unified data structures: Implements unified data structures and curated catalogs tailored for transcription factor analyses.
• Integration utilities: Includes utility functions to integrate TF annotations with genomic, transcriptomic, or regulatory datasets.

Scientific Applications:

• Gene regulatory analysis: Analyze gene regulatory mechanisms by combining TF annotations and binding data.
• GWAS integration: Integrate TF binding patterns with genome-wide association study (GWAS) results to interpret genetic associations.
• TF–target relationship analysis: Identify and examine TF–target associations using the MSigDb-derived catalog.
• Cross-dataset annotation: Cross-reference TF resources with genomic, transcriptomic, or regulatory datasets for comprehensive analyses.

Methodology:

Harmonizes TF catalogs from CISBP, HOCOMOCO, and Gene Ontology; derives a TF–target catalog from MSigDb; provides programmatic access to 690 ENCODE TF binding experiment results; and exposes unified data structures and utility functions for integration with genomic and transcriptomic datasets.