GREG

GREG integrates protein-DNA, protein-protein, non-coding RNA (ncRNA)-DNA, ncRNA-protein, and DNA-DNA interaction data into a graph database to model and explore transcriptional regulation.

Key Features:

• Comprehensive Interaction Network: Integrates protein-DNA, protein-protein, non-coding RNA (ncRNA)-DNA, ncRNA-protein, and DNA-DNA interactions into a single graph representation.
• Entity-centric Network Views: Provides network views centered on specific transcription factors, long non-coding RNAs (lncRNAs), genomic ranges, or DNA annotations.
• Visualization and Network Exploration: Enables visualization and exploration of regulatory networks to examine relationships among nodes and interactions.
• Advanced Graph Querying: Supports extraction of node and interaction information, identification of connected nodes, and execution of sophisticated graphical queries on the network.

Scientific Applications:

• Transcription factor regulatory landscape analysis: Applied to study the regulatory landscape of Nanog and its role in maintaining pluripotency in stem cells.
• Disease mechanism investigation: Used to explore regulatory mechanisms underlying complex diseases such as chronic obstructive pulmonary disease (COPD).

Methodology:

Integration and visualization of multiple interaction types within a graph database framework.