TY - JOUR
T1 - GSDB
T2 - a database of 3D chromosome and genome structures reconstructed from Hi-C data
AU - Oluwadare, Oluwatosin
AU - Highsmith, Max
AU - Turner, Douglass
AU - Lieberman-Aiden, Erez
AU - Cheng, Jianlin
PY - 2020/8/5
Y1 - 2020/8/5
N2 - Advances in the study of chromosome conformation capture technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional chromosome and genome structure reconstruction methods from Hi-C data. The three dimensional genome structure is important because it plays a role in a variety of important biological activities such as DNA replication, gene regulation, genome interaction, and gene expression. In recent years, numerous Hi-C datasets have been generated, and likewise, a number of genome structure construction algorithms have been developed. In this work, we outline the construction of a novel Genome Structure Database (GSDB) to create a comprehensive repository that contains 3D structures for Hi-C datasets constructed by a variety of 3D structure reconstruction tools. The GSDB contains over 50,000 structures from 12 state-of-the-art Hi-C data structure prediction algorithms for 32 Hi-C datasets. GSDB functions as a centralized collection of genome structures which will enable the exploration of the dynamic architectures of chromosomes and genomes for biomedical research. GSDB is accessible at http://sysbio.rnet.missouri.edu/3dgenome/GSDB.
AB - Advances in the study of chromosome conformation capture technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional chromosome and genome structure reconstruction methods from Hi-C data. The three dimensional genome structure is important because it plays a role in a variety of important biological activities such as DNA replication, gene regulation, genome interaction, and gene expression. In recent years, numerous Hi-C datasets have been generated, and likewise, a number of genome structure construction algorithms have been developed. In this work, we outline the construction of a novel Genome Structure Database (GSDB) to create a comprehensive repository that contains 3D structures for Hi-C datasets constructed by a variety of 3D structure reconstruction tools. The GSDB contains over 50,000 structures from 12 state-of-the-art Hi-C data structure prediction algorithms for 32 Hi-C datasets. GSDB functions as a centralized collection of genome structures which will enable the exploration of the dynamic architectures of chromosomes and genomes for biomedical research. GSDB is accessible at http://sysbio.rnet.missouri.edu/3dgenome/GSDB.
KW - 3C
KW - 3D chromosome structures
KW - 3D genome structures
KW - Database
KW - Genomics
KW - GSDB
KW - Hi-C
UR - http://www.scopus.com/inward/record.url?scp=85089170376&partnerID=8YFLogxK
U2 - 10.1186/s12860-020-00304-y
DO - 10.1186/s12860-020-00304-y
M3 - Article
C2 - 32758136
AN - SCOPUS:85089170376
VL - 21
JO - BMC Molecular and Cell Biology
JF - BMC Molecular and Cell Biology
IS - 1
M1 - 60
ER -