Deep learning model for predicting genetic diseases using DNA sequence data

Abstract

The emergence of machine learning in the recent decade has excelled in determining new potential features and nonlinear relationships existing between the data derived from the DNA sequences of genetic diseases. Machine learning also enhances the process of handling data with maximum predicted variables compared to observations during the data mining process of prediction. In this context, our study presents a deep learning model for predicting Transcription Factor Binding Sites (TFBS) in DNA sequences, with a focus on features within genetic data associated with diseases. Transcription Factors (TFs) play a crucial role in modulating gene expression by binding to TFBS. The accurate prediction of TFBS is essential for understanding genome function and evolution. Thus, we develop an efficient deep learning model that considers TFBS prediction as a nucleotide-level binary classification task. In our proposed model, first we create an input matrix using the original DNA sequences. Next, we encode these DNA sequences using one-hot encoding, representing them as a sequence of numerical values. We then employ three convolutional layers, allowing our model to capture intricate patterns and motif features over a larger spatial range. To capture important features within the DNA sequence and to focus on them, we incorporate an attention layer. Finally, a dense layer, consisting of two fully connected layers and a dropout layer, calculates the probability of TF binding site occurrence based on the features learned by the proposed model. Our experimental results, using in-vivo datasets obtained from Chip-seq, demonstrate the superior performance of our proposed deep learning model in TFBS prediction compared to other existing state-of-the-art methods. The improvement in accuracy is due to additional layers of CNN and then an attention layer in the model. Thus, this result in a better performance of our approach in predicting the transcription factor binding sites and enhancing our understanding of gene regulation and genome function.