Advantages of using graph databases to explore chromatin conformation capture experiments.

ABSTRACT:

Background

High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices describing the binary contacts among the different chromosome regions. On the other hand, a graph-based representation can be advantageous to describe the complex topology achieved by the DNA in the nucleus of eukaryotic cells.

Methods

Here we discuss the use of a graph database for storing and analysing data achieved by performing Hi-C experiments. The main issue is the size of the produced data and, working with a graph-based representation, the consequent necessity of adequately managing a large number of edges (contacts) connecting nodes (genes), which represen

SUBMITTER: D'Agostino D 

PROVIDER: S-EPMC8073886 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature