Abstract
A promoter is a short region of DNA (100–1,000 bp) where transcription of a gene by RNA polymerase begins. It is typically located directly upstream or at the 5′ end of the transcription initiation site. DNA promoter has been proven to be the primary cause of many human diseases, especially diabetes, cancer, or Huntington's disease. Therefore, classifying promoters has become an interesting problem and it has attracted the attention of a lot of researchers in the bioinformatics field. There were a variety of studies conducted to resolve this problem, however, their performance results still require further improvement. In this study, we will present an innovative approach by interpreting DNA sequences as a combination of continuous FastText N-grams, which are then fed into a deep neural network in order to classify them. Our approach is able to attain a cross-validation accuracy of 85.41 and 73.1% in the two layers, respectively. Our results outperformed the state-of-the-art methods on the same dataset, especially in the second layer (strength classification). Throughout this study, promoter regions could be identified with high accuracy and it provides analysis for further biological research as well as precision medicine. In addition, this study opens new paths for the natural language processing application in omics data in general and DNA sequences in particular.
Highlights
A promoter is a region of DNA where RNA polymerase begins to transcribe a gene
Promoter sequences are typically located directly upstream or at the 5′ end of the transcription initiation site (Lin et al, 2018). Both promoters and transcription initiation sites are bound by RNA polymerase and the necessary transcription factors
Many recent studies suggested that DNA promoters may be the primary cause of many human diseases, especially diabetes (Döhr et al, 2005; Ionescu-Tîrgoviste et al, 2015) or Huntington’s disease (Coles et al, 1998)
Summary
A promoter is a region of DNA where RNA polymerase begins to transcribe a gene. Promoter sequences are typically located directly upstream or at the 5′ end of the transcription initiation site (Lin et al, 2018). Both promoters and transcription initiation sites are bound by RNA polymerase and the necessary transcription factors. The transcription process is shown, which contains two steps: turning on and turning off genes. In these two stages, promoters receive information from RNA polymerase to decide the Classifying Promoters Using Deep Learning manufacture of lactase. Many recent studies suggested that DNA promoters may be the primary cause of many human diseases, especially diabetes (Döhr et al, 2005; Ionescu-Tîrgoviste et al, 2015) or Huntington’s disease (Coles et al, 1998)
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