Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.

ABSTRACT:

Motivation

Topologically associating domains (TADs) are fundamental building blocks of 3D genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity.

Results

We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data. It takes Hi-C contact matrix as the adjacency matrix for a graph, embeds the graph structures into a low-dimensional space with the help of sparse matrix factorization followed by spectral propagation, and the TAD-like domains can be i

SUBMITTER: Liu E 

PROVIDER: S-EPMC10960928 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature