Abstract
Transcription factor binding site (TFBS), one of the DNA-protein binding sites, plays important roles in understanding regulation of gene expression and drug design. Recently, deep-learning based methods have been widely used in the prediction of TFBS. In this work, we propose a novel deep-learning model, called Combination of Multi-Scale Convolutional Network and Long Short-Term Memory Network (MCNN-LSTM), which utilizes multi-scale convolution for feature processing, and the long short-term memory network to recognize TFBS in DNA sequences. Moreover, we design a new encoding method, called multi-nucleotide one-hot (MNOH), which considers the correlation between nucleotides in adjacent positions, to further improve the prediction performance of TFBS. Stringent cross-validation and independent tests on benchmark datasets demonstrated the efficacy of MNOH and MCNN-LSTM. Based on the proposed methods, we further implement a new TFBS predictor, called DeepTF. The computational experimental results show that our predictor outperformed several existing TFBS predictors.
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Acknowledgments
This work was supported by the National Natural Science Foundation of China (No. 61772273, 61373062) and the Fundamental Research Funds for the Central Universities (No. 30918011104).
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Bao, XR., Zhu, YH., Yu, DJ. (2019). DeepTF: Accurate Prediction of Transcription Factor Binding Sites by Combining Multi-scale Convolution and Long Short-Term Memory Neural Network. In: Cui, Z., Pan, J., Zhang, S., Xiao, L., Yang, J. (eds) Intelligence Science and Big Data Engineering. Big Data and Machine Learning. IScIDE 2019. Lecture Notes in Computer Science(), vol 11936. Springer, Cham. https://doi.org/10.1007/978-3-030-36204-1_10
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