DeepCNPP: Deep Learning Architecture to Distinguish the Promoter of Human Long Non-Coding RNA Genes and Protein-Coding Genes

Tanvir Alam*, Mohammad Tariqul Islam, Mowafa Househ, Samir Brahim Belhaouari, Ferdaus Ahmed Kawsar

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

5 Citations (Scopus)

Abstract

Promoter region of protein-coding genes are gradually being well understood, yet no comparable studies exist for the promoter of long non-coding RNA (lncRNA) genes which has emerged as a global potential regulator in multiple cellular process and different diseases for human. To understand the difference in the transcriptional regulation pattern of these genes, previously, we proposed a machine learning based model to classify the promoter of protein-coding genes and lncRNA genes. In this study, we are presenting DeepCNPP (deep coding non-coding promoter predictor), an improved model based on deep learning (DL) framework to classify the promoter of lncRNA genes and protein-coding genes. We used convolution neural network (CNN) based deep network to classify the promoter of these two broad categories of human genes. Our computational model, built upon the sequence information only, was able to classify these two groups of promoters from human at a rate of 83.34% accuracy and outperformed the existing model. Further analysis and interpretation of the output from DeepCNPP architecture will enable us to understand the difference in transcription regulatory pattern for these two groups of genes.

Original languageEnglish
Title of host publicationHealth Informatics Vision
Subtitle of host publicationFrom Data via Information to Knowledge
EditorsJohn Mantas, Arie Hasman, Parisis Gallos, Aikaterini Kolokathi, Mowafa S. Househ, Joseph Liaskos
PublisherIOS Press
Pages232-235
Number of pages4
ISBN (Electronic)9781614999867
DOIs
Publication statusPublished - 2019

Publication series

NameStudies in Health Technology and Informatics
Volume262
ISSN (Print)0926-9630
ISSN (Electronic)1879-8365

Keywords

  • Convolution neural network
  • Deep learning
  • Long non-coding RNA
  • Promoter

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