| Autor: |
Van Hovenga, Jugal Kalita, Oluwatosin Oluwadare |
| Jazyk: |
angličtina |
| Rok vydání: |
2023 |
| Předmět: |
|
| Zdroj: |
Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 812-836 (2023) |
| Druh dokumentu: |
article |
| ISSN: |
2001-0370 |
| DOI: |
10.1016/j.csbj.2022.12.051 |
| Popis: |
Chromosome conformation capture (3 C) is a method of measuring chromosome topology in terms of loci interaction. The Hi-C method is a derivative of 3 C that allows for genome-wide quantification of chromosome interaction. From such interaction data, it is possible to infer the three-dimensional (3D) structure of the underlying chromosome. In this paper, we developed a novel method, HiC-GNN, for predicting the 3D structures of chromosomes from Hi-C data. HiC-GNN is unique from other methods for chromosome structure prediction in that the models learned by HiC-GNN can be generalized to data that is distinct from the training data. This aspect of HiC-GNN allows models that were trained on one Hi-C contact map to be used for inference on entirely different maps. To the authors’ knowledge, this generalizing capability is not present in any existing methods. HiC-GNN uses a node embedding algorithm and a graph neural network to predict the 3D coordinates of each genomic loci from the corresponding Hi-C contact data. Unlike other methods, our algorithm allows for the storage of pre-trained parameters, thus enabling prediction on data that is entirely different from the training data. We show that our method can accurately generalize a single model across Hi-C resolutions, multiple restriction enzymes, and multiple cell populations while maintaining reconstruction accuracy across three Hi-C datasets. Our algorithm outperforms the state-of-the-art methods in accuracy of prediction and runtime and introduces a novel method for 3D structure prediction from Hi-C data. All our source codes and data are available at https://github.com/OluwadareLab/HiC-GNN. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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