Epoch

Epoch reconstructs dynamic gene regulatory networks from single-cell transcriptomic data to capture transitions in regulatory topology and identify regulators driving cell-fate decisions.

Key Features:

• Dynamic Network Inference: Infers dynamic structures of gene regulatory networks (GRNs) from single-cell transcriptomic datasets and captures transitions between network topologies.
• Single-Cell Transcriptomics Integration: Integrates single-cell transcriptomic data from in vivo, in vitro, and in silico sources to reconstruct network dynamics across experimental conditions.
• Benchmark Performance: Has been benchmarked on datasets from multiple biological contexts to assess robustness and accuracy.

Scientific Applications:

• Transcription Factor–Target Relationships: Elucidates regulatory relationships between transcription factors (TFs) and target genes using reconstructed GRNs.
• Directed Differentiation of Embryonic Stem Cells: Applied to study directed differentiation of mouse embryonic stem cells (ESCs) under primitive streak induction treatments to identify networks that drive cell-fate decisions.
• Signaling Pathway Integration: Integrates signaling pathways with GRN structures to trace how pathway activations or suppressions (e.g., Wnt activation, PI3K suppression) influence cellular specification.
• Mesoderm Specification: Identifies contributors to network rewiring such as Peg3 in the context of mesoderm specification during ESC differentiation.

Methodology:

Maps regulatory relationships from single-cell transcriptomic data, reconstructs network topologies, identifies key contributors to network rewiring (for example, Peg3 in mesoderm specification), compares networks established under different experimental conditions, and integrates data from in vivo, in vitro, and in silico sources.