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Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences.
- Source :
-
Genome biology [Genome Biol] 2021 Aug 16; Vol. 22 (1), pp. 226. Date of Electronic Publication: 2021 Aug 16. - Publication Year :
- 2021
-
Abstract
- Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chromatin interactions between open chromatin regions using only DNA sequences. ChINN predicts CTCF- and RNA polymerase II-associated and Hi-C chromatin interactions. ChINN shows good across-sample performances and captures various sequence features for chromatin interaction prediction. We apply ChINN to 6 chronic lymphocytic leukemia (CLL) patient samples and a published cohort of 84 CLL open chromatin samples. Our results demonstrate extensive heterogeneity in chromatin interactions among CLL patient samples.<br /> (© 2021. The Author(s).)
Details
- Language :
- English
- ISSN :
- 1474-760X
- Volume :
- 22
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Genome biology
- Publication Type :
- Academic Journal
- Accession number :
- 34399797
- Full Text :
- https://doi.org/10.1186/s13059-021-02453-5