3DGene

3DGene stores and provides access to predicted 3D conformations of active gene topoi in GM12878 human lymphoblastoid cells for investigating relationships between chromatin structure and gene function.

Key Features:

• 3D Structure Database: Contains predicted 3D conformations of over 10,000 active gene topoi predicted by the e-HiP-HoP framework.
• Topos Definition: Defines and stores "topoi" as 3D structural units representing the regulatory landscape around gene promoters.
• Structural Diversity Scoring: Computes a structural diversity score to quantify variation in chromatin conformations.
• Influential Node Identification: Identifies influential nodes as chromatin sites that frequently interact with gene promoters and drive structural diversity.
• Folding Motif Analysis: Reveals folding motifs and their links to Gene Ontology features through data mining.

Scientific Applications:

• Gene Structure-Function Analysis: Investigates the relationship between 3D gene structure and function through predicted chromatin conformations.
• Regulatory Network Mapping: Reveals insights into gene regulatory networks by analyzing chromatin contact networks around gene promoters.
• Chromatin Architecture Prediction: Provides a framework for modeling high-resolution chromatin structure using epigenetic data.

Methodology:

The e-HiP-HoP (epigenetic highly predictive heteromorphic polymer) model predicts 3D chromatin structure based on genome organization principles, using GM12878 cell data to generate gene topoi structures.