MethylNet: an automated and modular deep learning approach for DNA methylation analysis
By Joshua J. Levy, A. Titus, Curtis L. Petersen, Youdinghuan Chen, L. Salas, Brock C. Christensen. 2019
118 citations recorded by the source corpus.
DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations with phenotypes suffer from multiple hypothesis testing and multi-collinearity due to the high-dimensional, continuous, interacting and non-linear nature of the data. Deep learning analyses have shown much promise to study disease heterogeneity. DNAm deep learning approaches have not yet been formalized into user-friendly frameworks for execution, training, and interpreting models. Here, we describe MethylNet, a DNAm deep learning method that can construct embeddings, make predictions, generate new data, and uncover unknown heterogeneity with minimal user supervision. The results of our experiments indicate that MethylNet can study cellular differences, grasp higher order information of cancer sub-types, estimate age and capture factors associated with smoking in concordance with known differences. The ability of MethylNet to capture nonlinear interactions presents an opportunity for further study of unknown disease, cellular heterogeneity and aging processes.
Subfields: Genetics, Molecular Biology, Computational Biology & Bioinformatics
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Citations in the corpus
- Big Bird: Transformers for Longer Sequences (2020, background): “…has been a recent upsurge in using deep learning for genomics data [87, 107, 13], which has resulted in improved performance on several biologically-significant tasks such as promoter site prediction [71], methylation analysis [55], predicting functional effects of non-coding variant [110], etc.”
- Deep learning in cancer diagnosis, prognosis and treatment selection (2021, methodology): “Recently developed DL TME methods include Scaden [71], a transcriptomic-based neural network model, and MethylNet, a methylation-based model [72].”