RT networks

RT networks is a software tool that allows users to construct and analyze different types of replication timing (RT) regulatory networks using genome-wide RT profiles from various human cell types and differentiation stages. The main features and capabilities of RT networks are:

1. Coordinated RT change networks: RT networks can create complex networks based on coordinated changes in replication timing during cell differentiation. These networks consist of numerous interactions forming distinct functional subnetwork communities.

2. Directional regulatory networks: The tool can construct directional networks based on the sequential order of RT changes within cell lineages, enabling the identification of master regulators driving differentiation pathways.

3. Integration with transcriptional regulatory networks (TRNs): RT networks can explore the relationships between RT networks and TRNs by combining them into composite and bipartite networks, providing insights into the complex gene regulation circuitry.

4. Utilization of diverse data: The software uses genome-wide RT profiles from 15 human cell types and intermediate differentiation stages derived from human embryonic stem cells, allowing for a comprehensive analysis of RT regulation during development.