Literature DB >> 33420191

DNA sequences performs as natural language processing by exploiting deep learning algorithm for the identification of N4-methylcytosine.

Abdul Wahab1, Hilal Tayara2, Zhenyu Xuan3, Kil To Chong4,5.   

Abstract

N4-methylcytosine is a biochemical alteration of DNA that affects the genetic operations without modifying the DNA nucleotides such as gene expression, genomic imprinting, chromosome stability, and the development of the cell. In the proposed work, a computational model, 4mCNLP-Deep, used the word embedding approach as a vector formulation by exploiting deep learning based CNN algorithm to predict 4mC and non-4mC sites on the C.elegans genome dataset. Diversity of ranges employed for the experimental such as corpus k-mer and k-fold cross-validation to obtain the prevailing capabilities. The 4mCNLP-Deep outperform from the state-of-the-art predictor by achieving the results in five evaluation metrics by following; Accuracy (ACC) as 0.9354, Mathew's correlation coefficient (MCC) as 0.8608, Specificity (Sp) as 0.89.96, Sensitivity (Sn) as 0.9563, and Area under curve (AUC) as 0.9731 by using 3-mer corpus word2vec and 3-fold cross-validation and attained the increment of 1.1%, 0.6%, 0.58%, 0.77%, and 4.89%, respectively. At last, we developed the online webserver http://nsclbio.jbnu.ac.kr/tools/4mCNLP-Deep/ , for the experimental researchers to get the results easily.

Entities:  

Year:  2021        PMID: 33420191      PMCID: PMC7794489          DOI: 10.1038/s41598-020-80430-x

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  36 in total

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4.  iRNA-PseKNC(2methyl): Identify RNA 2'-O-methylation sites by convolution neural network and Chou's pseudo components.

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Journal:  J Theor Biol       Date:  2018-12-24       Impact factor: 2.691

Review 5.  Establishing, maintaining and modifying DNA methylation patterns in plants and animals.

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Journal:  Nat Rev Genet       Date:  2010-03       Impact factor: 53.242

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7.  Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment.

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9.  iMethyl-Deep: N6 Methyladenosine Identification of Yeast Genome with Automatic Feature Extraction Technique by Using Deep Learning Algorithm.

Authors:  Omid Mahmoudi; Abdul Wahab; Kil To Chong
Journal:  Genes (Basel)       Date:  2020-05-09       Impact factor: 4.096

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  6 in total

1.  BERT-m7G: A Transformer Architecture Based on BERT and Stacking Ensemble to Identify RNA N7-Methylguanosine Sites from Sequence Information.

Authors:  Lu Zhang; Xinyi Qin; Min Liu; Guangzhong Liu; Yuxiao Ren
Journal:  Comput Math Methods Med       Date:  2021-08-25       Impact factor: 2.238

2.  Systematic Analysis and Accurate Identification of DNA N4-Methylcytosine Sites by Deep Learning.

Authors:  Lezheng Yu; Yonglin Zhang; Li Xue; Fengjuan Liu; Qi Chen; Jiesi Luo; Runyu Jing
Journal:  Front Microbiol       Date:  2022-03-15       Impact factor: 5.640

3.  Online Diagnosis and Classification of CT Images Collected by Internet of Things Using Deep Learning.

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Review 5.  Representation learning applications in biological sequence analysis.

Authors:  Hitoshi Iuchi; Taro Matsutani; Keisuke Yamada; Natsuki Iwano; Shunsuke Sumi; Shion Hosoda; Shitao Zhao; Tsukasa Fukunaga; Michiaki Hamada
Journal:  Comput Struct Biotechnol J       Date:  2021-05-23       Impact factor: 7.271

6.  Construction and Validation of a Lung Cancer Diagnostic Model Based on 6-Gene Methylation Frequency in Blood, Clinical Features, and Serum Tumor Markers.

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Journal:  Comput Math Methods Med       Date:  2021-06-26       Impact factor: 2.238

  6 in total

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