GSDB

GSDB catalogs three-dimensional chromosome and genome structures reconstructed from Hi-C contact data to enable analysis of genome architecture.

Key Features:

• Repository scale: Contains over 50,000 reconstructed 3D genome and chromosome structures.
• Hi-C source data: Structures are derived from 32 distinct Hi-C datasets capturing genome-wide chromosomal interactions.
• Multiple reconstruction algorithms: Includes structures generated using 12 distinct structure prediction algorithms.
• Structure scope: Covers chromosome- and genome-scale three-dimensional conformations.
• Originating laboratory: Compiled and maintained by the Bioinformatics, Data Mining, Machine Learning (BDM) Laboratory.

Scientific Applications:

• Genome architecture analysis: Enables investigation of three-dimensional chromosomal organization.
• Regulation and expression studies: Supports analyses related to DNA replication, gene regulation, and gene expression using 3D structural context.
• Comparative method assessment: Facilitates comparative studies of 3D reconstruction algorithms across multiple Hi-C datasets.
• Biomedical research: Supports research into the implications of genomic organization in health and disease.

Methodology:

Structures were reconstructed from Hi-C contact data using 12 structure prediction algorithms across 32 Hi-C datasets and compiled into the GSDB repository, totaling over 50,000 structures.