ESCDb

ESCDb consolidates datasets on human and mouse embryonic stem cells (ESCs) and embryonal carcinoma (EC) cell lines to support analysis of transcription factor regulation and gene‑regulatory modules.

Key Features:

• Dataset Collection: Aggregates perturbation experiments including knock-down and overexpression studies and ChIP experiments conducted on ESCs and EC cell lines.
• Transcription Factor Binding Data: Integrates ChIP-PET, ChIP-chip, and ChIP-seq datasets for detailed mapping of transcription factor binding sites.
• OCT4 Network Analysis: Provides refined lists of OCT4 targets identified through CHIP-on-chip analysis and validated by comparison with existing datasets.
• Motif-Specific Modules: Identifies a POU-motif associated with OCT4 binding and defines six motif-driven regulatory modules relevant to stem cell expression programs.
• Validation of Targets: Includes validated targets such as NANOG with an evolutionarily conserved OCT4-SOX2 binding motif and genes like USP44 and GADD45G lacking the classical HMG motif but implicated in cell cycle regulation and development.
• Systems Biology Integration: Integrates human and mouse ESC and EC datasets to enable comparative analysis of OCT4 targets across cell types.

Scientific Applications:

• Regenerative Medicine: Facilitates analysis of transcription factor networks and target genes relevant to stem cell self-renewal and differentiation.
• Cancer Research: Supports investigation of molecular mechanisms in embryonal carcinoma (EC) cell lines related to proliferation and differentiation.
• Stem Cell Biology: Enables exploration of OCT4-centered regulatory networks, motif-driven modules, and validated targets underlying stem cell maintenance.

Methodology:

Collection of ChIP experiments and RNAi-based ablation studies with dataset integration performed using peak analysis programs.