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. 2015 Sep 7:5:13859.
doi: 10.1038/srep13859.

Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome

Wei Chen  1   2 , Hong Tran  2 , Zhiyong Liang  3 , Hao Lin  3 , Liqing Zhang  2
Affiliations

Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome

Wei Chen et al. Sci Rep. .

Abstract

Knowledge of the distribution of N(6)-methyladenosine (m(6)A) is invaluable for understanding RNA biological functions. However, limitation in experimental methods impedes the progress towards the identification of m(6)A site. As a complement of experimental methods, a support vector machine based-method is proposed to identify m(6)A sites in Saccharomyces cerevisiae genome. In this model, RNA sequences are encoded by their nucleotide chemical property and accumulated nucleotide frequency information. It is observed in the jackknife test that the accuracy achieved by the proposed model in identifying the m(6)A site was 78.15%. For the convenience of experimental scientists, a web-server for the proposed model is provided at http://lin.uestc.edu.cn/server/m6Apred.php.

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Figures

Figure 1
Figure 1. Sequence logo of the 10 upstream and 10 downstream nucleotides surrounding m6A sites.
Figure 2
Figure 2. A graphical illustration to show the performance of the model by means of the ROC curve.
The vertical coordinate is the true positive rate (Sn) while horizontal coordinate is the false positive rate (1-Sp). The area under the ROC curve (AUROC) is 0.84.
Figure 3
Figure 3. A semi-screenshot for the top page of the web-server at http://lin.uestc.edu.cn/server/m6Apred.php.
Figure 4
Figure 4. Chemical structure of each nucleotide.
See this image and copyright information in PMC

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