dbEmbryo

dbEmbryo integrates a multi-omics compendium of gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure to enable analysis of epigenetic regulation during early human and mouse embryo development.

Key Features:

• Multi-Omics Integration: Consolidates gene expression, DNA methylation, histone modification, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse embryos.
• Multi-omics Visualization: Provides visualization of interactions across multiple omics layers to examine spatiotemporal relationships.
• Gene & Peak Annotation: Annotates genes and associated epigenetic peaks to link genomic features with regulatory signals.
• ZGA Gene Cluster Analysis: Analyzes zygotic genome activation (ZGA) gene clusters to characterize transcriptional changes during early embryonic stages.
• Cis-Regulation and Synergistic Regulation Tools: Supports analysis of cis-regulatory elements and synergistic regulation among epigenetic markers.
• Promoter Signal Enrichment Analysis: Quantifies enrichment of regulatory signals within promoter regions.
• 3D Genome Exploration: Enables examination of higher-order chromatin structure and its influence on gene regulation.

Scientific Applications:

• Modeling Transcriptional Control: Facilitates development of models of transcriptional control during early embryo development using integrated omics signals.
• Deciphering Molecular Regulatory Mechanisms: Enables investigation of coordinated epigenetic mechanisms that regulate gene expression in early embryos.
• Comparative Analysis Across Species: Supports comparative analyses of human and mouse embryonic omics to identify conserved and divergent regulatory features.

Methodology:

Integrates multi-layered omics data into a framework for analysis of synergistic changes in gene expression and epigenetic profiles to explore coordinated epigenetic regulation during early development.