An Effective Deep Learning-Based Architecture for Prediction of N7-Methylguanosine Sites in Health Systems

被引:2
作者
Tahir, Muhammad [1 ]
Hayat, Maqsood [1 ]
Khan, Rahim [1 ]
Chong, Kil To [2 ,3 ]
机构
[1] Abdul Wali Khan Univ Mardan, Dept Comp Sci, Mardan 23200, Pakistan
[2] Jeonbuk Natl Univ, Dept Elect & Informat Engn, Jeonju 54896, South Korea
[3] Chonbuk Natl Univ, Adv Elect & Informat Res Ctr, Jeonju 54896, South Korea
基金
新加坡国家研究基金会;
关键词
deep learning; pattern recognition; LSTM; RNA; natural language processing; CONVOLUTION NEURAL-NETWORK; RNA; MODEL;
D O I
10.3390/electronics11121917
中图分类号
TP [自动化技术、计算机技术];
学科分类号
0812 ;
摘要
N-7-methylguanosine (m7G) is one of the most important epigenetic modifications found in rRNA, mRNA, and tRNA, and performs a promising role in gene expression regulation. Owing to its significance, well-equipped traditional laboratory-based techniques have been performed for the identification of N-7-methylguanosine (m7G). Consequently, these approaches were found to be time-consuming and cost-ineffective. To move on from these traditional approaches to predict N-7 methylguanosine sites with high precision, the concept of artificial intelligence has been adopted. In this study, an intelligent computational model called N-7-methylguanosine-Long short-term memory (m7G-LSTM) is introduced for the prediction of N-7-methylguanosine sites. One-hot encoding and word2vec feature schemes are used to express the biological sequences while the LSTM and CNN algorithms have been employed for classification. The proposed "m7G-LSTM" model obtained an accuracy value of 95.95%, a specificity value of 95.94%, a sensitivity value of 95.97%, and Matthew's correlation coefficient (MCC) value of 0.919. The proposed predictive m7G-LSTM model has significantly achieved better outcomes than previous models in terms of all evaluation parameters. The proposed m7G-LSTM computational system aims to support the drug industry and help researchers in the fields of bioinformatics to enhance innovation for the prediction of the behavior of N-7-methylguanosine sites.
引用
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页数:11
相关论文
共 63 条
[1]  
Bai S., EMPIRICAL EVALUATION
[2]   An Interpretable Prediction Model for Identifying N7-Methylguanosine Sites Based on XGBoost and SHAP [J].
Bi, Yue ;
Xiang, Dongxu ;
Ge, Zongyuan ;
Li, Fuyi ;
Jia, Cangzhi ;
Song, Jiangning .
MOLECULAR THERAPY-NUCLEIC ACIDS, 2020, 22 :362-372
[3]   iRNA-m7G: Identifying N7-methylguanosine Sites by Fusing Multiple Features [J].
Chen, Wei ;
Feng, Pengmian ;
Song, Xiaoming ;
Lv, Hao ;
Lin, Hao .
MOLECULAR THERAPY-NUCLEIC ACIDS, 2019, 18 :269-274
[4]   iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties [J].
Chen, Wei ;
Yang, Hui ;
Feng, Pengmian ;
Ding, Hui ;
Lin, Hao .
BIOINFORMATICS, 2017, 33 (22) :3518-3523
[5]   iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences [J].
Chen, Wei ;
Feng, Pengmian ;
Yang, Hui ;
Ding, Hui ;
Lin, Hao ;
Chou, Kuo-Chen .
ONCOTARGET, 2017, 8 (03) :4208-4217
[6]   iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition [J].
Chen, Wei ;
Feng, Peng-Mian ;
Lin, Hao ;
Chou, Kuo-Chen .
NUCLEIC ACIDS RESEARCH, 2013, 41 (06) :e68
[7]   G2Vec: Distributed gene representations for identification of cancer prognostic genes [J].
Choi, Jonghwan ;
Oh, Ilhwan ;
Seo, Sangmin ;
Ahn, Jaegyoon .
SCIENTIFIC REPORTS, 2018, 8
[8]   Regulation of mRNA cap methylation [J].
Cowling, Victoria H. .
BIOCHEMICAL JOURNAL, 2010, 425 :295-302
[9]   Iterative feature representation algorithm to improve the predictive performance of N7-methylguanosine sites [J].
Dai, Chichi ;
Feng, Pengmian ;
Cui, Lizhen ;
Su, Ran ;
Chen, Wei ;
Wei, Leyi .
BRIEFINGS IN BIOINFORMATICS, 2021, 22 (04)
[10]   Deep learning architectures for prediction of nucleosome positioning from sequences data [J].
Di Gangi, Mattia ;
Lo Bosco, Giosue ;
Rizzo, Riccardo .
BMC BIOINFORMATICS, 2018, 19