TcoFBase

TcofBase catalogs transcription co-factors (TcoFs) and integrates ChIP-seq-derived binding and (epi)genetic annotations for human and mouse to support analysis of TcoF-mediated gene regulation.

Key Features:

• Extensive Data Collection: Curates 2,322 TcoFs and 6,759 associated ChIP-seq datasets derived from over 500 tissues and cell types in human and mouse.
• Detailed Annotations: Provides (epi)genetic annotations of TcoF binding regions identified through ChIP-seq.
• Regulatory and Functional Annotations: Supplies regulatory annotation information and diverse functional annotations for TcoFs.
• Advanced Analytical Tools: Implements five analysis types to examine TcoF-related regulation:
  TcoF Gene Set Enrichment Analysis: Identifies enriched gene sets associated with specific TcoFs.
  TcoF Binding Genomic Region Annotation: Annotates genomic regions bound by TcoFs.
  TcoF Regulatory Network Analysis: Explores regulatory networks involving TcoFs.
  TcoF-TF Co-occupancy Analysis: Examines co-occupancy patterns between TcoFs and transcription factors (TFs).
  TcoF Regulatory Axis Analysis: Investigates potential regulatory axes involving TcoFs.

Scientific Applications:

• Functional characterization of TcoFs: Supports investigation of the biological effects and functional roles of TcoFs in gene regulation.
• Regulatory network analysis: Enables exploration of complex regulatory networks and interactions involving TcoFs and TFs.
• Disease and cellular process studies: Facilitates studies into how TcoFs contribute to cellular processes and disease mechanisms.

Methodology:

Collects and curates ChIP-seq datasets, identifies TcoF binding regions from ChIP-seq, and performs analyses including gene set enrichment, genomic region annotation, regulatory network analysis, TcoF–TF co-occupancy analysis, and regulatory axis analysis.