Classifying Promoters by Interpreting the Hidden Information of DNA Sequences via Deep Learning and Combination of Continuous FastText N-Grams

Nguyen Quoc Khanh Le, Edward Kien Yee Yapp, N. Nagasundaram, Hui Yuan Yeh

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number305
JournalFrontiers in Bioengineering and Biotechnology
Volume7
DOIs
Publication statusPublished - Nov 5 2019

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Keywords

  • convolutional neural network
  • DNA promoter
  • natural language processing
  • precision medicine
  • transcription factor
  • word embedding

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Histology
  • Biomedical Engineering

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