PromID: human promoter prediction by deep learning
This work addresses the challenge of reliable promoter identification in genomics, which is crucial for understanding gene regulation, but it is incremental as it builds on prior deep learning approaches.
The authors tackled the problem of predicting human promoters in long genomic sequences by developing a deep learning model that predicts exact transcription start site positions, achieving a recall of 0.76, precision of 0.77, and MCC of 0.76, significantly outperforming existing tools like FPROM.
Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initiation complex. While there are many attempts to develop computational promoter identification methods, we have no reliable tool to analyze long genomic sequences. In this work we further develop our deep learning approach that was relatively successful to discriminate short promoter and non-promoter sequences. Instead of focusing on the classification accuracy, in this work we predict the exact positions of the TSS inside the genomic sequences testing every possible location. We studied human promoters to find effective regions for discrimination and built corresponding deep learning models. These models use adaptively constructed negative set which iteratively improves the models discriminative ability. The developed promoter identification models significantly outperform the previously developed promoter prediction programs by considerably reducing the number of false positive predictions. The best model we have built has recall 0.76, precision 0.77 and MCC 0.76, while the next best tool FPROM achieved precision 0.48 and MCC 0.60 for the recall of 0.75. Our method is available at http://www.cbrc.kaust.edu.sa/PromID/.