EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning

Abstract

Background N6, 2'-O-dimethyladenosine (m6Am) is an abundant RNA methylation modification on vertebrate mRNAs and is present in the transcription initiation region of mRNAs. It has recently been experimentally shown to be associated with several human disorders, including obesity genes, and stomach cancer, among others. As a result, N6,2′-O-dimethyladenosine (m6Am) site will play a crucial part in the regulation of RNA if it can be correctly identified. Results This study proposes a novel deep learning-based m6Am prediction model, EMDL_m6Am, which employs one-hot encoding to expressthe feature map of the RNA sequence and recognizes m6Am sites by integrating different CNN models via stacking. Including DenseNet, Inflated Convolutional Network (DCNN) and Deep Multiscale Residual Network (MSRN), the sensitivity (Sn), specificity (Sp), accuracy (ACC), Mathews correlation coefficient (MCC) and area under the curve (AUC) of our model on the training data set reach 86.62%, 88.94%, 87.78%, 0.7590 and 0.8778, respectively, and the prediction results on the independent test set are as high as 82.25%, 79.72%, 80.98%, 0.6199, and 0.8211. Conclusions In conclusion, the experimental results demonstrated that EMDL_m6Am greatly improved the predictive performance of the m6Am sites and could provide a valuable reference for the next part of the study. The source code and experimental data are available at: https://github.com/13133989982/EMDL-m6Am.

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“…One-Hot Encoding is one of the most frequently used methods for sequence data preprocessing [23][24][25]. It is a representation of categorical variables as binary vectors, which in detail means that categorical values are mapped to integer values, each represented as a binary vector, with all values being 0 except for one valid value, which is encoded as 1.…”

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