A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns

• Published in: Scientific reports Vol. 12; no. 1; p. 15183
• Main Authors: Butt, Ahmad Hassan, Alkhalifah, Tamim, Alturise, Fahad, Khan, Yaser Daanial
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 07-09-2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/114/1305; 631/114/1386; 631/114/2397; Bioinformatics; Deoxyribonucleic acid; DNA; Enhancers; Gene expression; Humanities and Social Sciences; multidisciplinary; Nucleotide sequence; Science; Science (multidisciplinary); Statistics
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-19099-3

Enhancers regulate gene expression, by playing a crucial role in the synthesis of RNAs and proteins. They do not directly encode proteins or RNA molecules. In order to control gene expression, it is important to predict enhancers and their potency. Given their distance from the target gene, lack of common motifs, and tissue/cell specificity, enhancer regions are thought to be difficult to predict in DNA sequences. Recently, a number of bioinformatics tools were created to distinguish enhancers from other regulatory components and to pinpoint their advantages. However, because the quality of its prediction method needs to be improved, its practical application value must also be improved. Based on nucleotide composition and statistical moment-based features, the current study suggests a novel method for identifying enhancers and non-enhancers and evaluating their strength. The proposed study outperformed state-of-the-art techniques using fivefold and tenfold cross-validation in terms of accuracy. The accuracy from the current study results in 86.5% and 72.3% in enhancer site and its strength prediction respectively. The results of the suggested methodology point to the potential for more efficient and successful outcomes when statistical moment-based features are used. The current study's source code is available to the research community at
https://github.com/csbioinfopk/enpred
.