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1.WHISTLE: A Functionally Annotated High-Accuracy Map of Human m6A Epitranscriptome

Author:Xu,Qingru;Chen,Kunqi;Meng,Jia

Source:Methods in Molecular Biology,2021,Vol.2284

Abstract:N6-Methyladenosine (m6A) is the most prevalent posttranscriptional modification in eukaryotes and plays a pivotal role in various biological processes, such as splicing, RNA degradation, and RNA–protein interaction. Accurately identification of the location of m6A is essential for related downstream studies. In this chapter, we introduce a prediction framework WHISTLE, which enables us to acquire so far the most accurate map of the transcriptome-wide human m6A RNA-methylation sites (with an average AUC: 0.948 and 0.880 under the full transcript or mature messenger RNA models, respectively, when tested on independent datasets). Besides, each individual m6A site was also functionally annotated according to the “guilt-by-association” principle by integrating RNA methylation data, gene expression data and protein–protein interaction data. A web server was constructed for conveniently querying the predicted RNA methylation sites and their putative biological functions. The website supports the query by genes, by GO function, table view, and the download of all the functionally annotated map of predicted map of human m6A epitranscriptome. The WHISTLE web server is freely available at: www.xjtlu.edu.cn/biologicalsciences/whistle and http://whistle-epitranscriptome.com.

2.MeT-DB V2.0: Elucidating Context-Specific Functions of N6-Methyl-Adenosine Methyltranscriptome

Author:Liu,Hui;Ma,Jiani;Meng,Jia;Zhang,Lin

Source:Methods in Molecular Biology,2021,Vol.2284

Abstract:N6-methyladenosine (m6A) is the most prevalent posttranscriptional modification in eukaryotes and plays a pivotal role in various biological processes. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. In this chapter, we present a comprehensive platform MeT-DB V2.0 for elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. Met-DB V2.0 database contains context specific m6A peaks and single-base sites predicted from 185 samples for 7 species from 26 independent studies. Moreover, it is also integrated with a new database for targets of m6A readers, erasers and writers and expanded with more collections of functional data. The Met-DB V2.0 web interface and genome browser provide more friendly, powerful, and informative ways to query and visualize the data. More importantly, MeT-DB V2.0 offers for the first time a series of tools specifically designed for understanding m6A functions. The MeT-DB V2.0 web server is freely available at: http://compgenomics.utsa.edu/MeTDB and www.xjtlu.edu.cn/metdb2.
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