Chromatin Interaction Neural Network (ChINN): A machine learning-based method for predicting chromatin interactions from DNA sequences
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ABSTRACT: Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. Various computational methods have been developed to predict chromatin interactions. Most of these methods rely on large collections of ChIP-Seq/RNA-Seq/DNase-Seq datasets and predict only enhancer-promoter interactions. Some of the ‘state-of-the-art’ methods have poor experimental designs, leading to over-exaggerated performances and misleading conclusions. Here we developed a computational method, Chromatin Interaction Neural Network (CHINN), to predict chromatin interactions between open chromatin regions by using only DNA sequences of the interacting open chromatin regions. CHINN is able to predict CTCF-, RNA polymerase II- and HiC-associated chromatin interactions between open chromatin regions. CHINN also shows good across-sample performances and captures various sequence features that are predictive of chromatin interactions. We applied CHINN to 90 chronic lymphocytic leukemia (CLL) samples and detected systematic differences in the chromatin interactome between IGVH-mutated and IGVH-unmutated CLL samples.
ORGANISM(S): Homo sapiens
PROVIDER: GSE163896 | GEO | 2021/07/09
REPOSITORIES: GEO
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