A Review About Transcription Factor Binding Sites Prediction Based on Deep Learning

Transcription factors (TFs) recognize and bind to specific DNA sequences, thereby altering the chromatin structure and regulating transcription. TFs aid in the formation of a guide genome that facilitates the expression of genes under complex regulation. Understanding the underlying mechanism that mediates the TF-led regulation of gene expression is a popular topic in current genomic research. However, identifying the precise TF binding site (TFBS) and the specific role of the TFs in transcriptional regulation is challenging. This article summarizes the status of research concerning the prediction of TFBS. First, the experimental methods for identifying TFBS have been summarized by accessing related databases. Second, the machine learning methods for predicting TFBS, especially deep learning, have been summarized. Finally, the study elaborates on the main challenges faced in TFBS prediction. The purpose of this article is to provide researchers with a comprehensively understand the prediction of TFBS and to promote further development in this field.