m6Aexpress-Reader : Prediction of m 6 A regulated expression genes by integrating m 6 A sites and reader binding information in specific- context
Methods, ISSN: 1046-2023, Vol: 203, Page: 167-178
2022
- 2Citations
- 4Captures
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Article Description
N 6 -methyladenosine (m 6 A) is the most abundant form of mRNA modification and plays an important role in regulating gene expression. However, the mechanisms of m 6 A regulated gene expression in cell or condition specific, are still poorly understood. Even though, some methods are able to predict m 6 A regulated expression (m 6 A-reg-exp) genes in specific context, they don’t introduce the m 6 A reader binding information, while this information can help to predict m 6 A-reg-exp genes and more clearly to explain the mechanisms of m 6 A-mediated gene expression process. Thus, by integrating m 6 A sites and reader binding information, we proposed a novel method (called m6Aexpress-Reader ) to predict m 6 A-reg-exp genes from limited MeRIP-seq data in specific context. m6Aexpress-Reader adopts the reader binding signal strength to weight the posterior distribution of the estimated regulatory coefficients for enhancing the prediction power. By using m6Aexpress-Reader, we found the complex characteristic of m 6 A on gene expression regulation and the distinct regulated pattern of m 6 A-reg-exp genes with different reader binding. m 6 A readers, YTHDF2 or IGF2BP1/3 all play an important role in various cancers and the key cancer pathways. In addition, m6Aexpress-Reader reveals the distinct m 6 A regulated mode of reader targeted genes in cancer. m6Aexpress-Reader could be a useful tool for studying the m 6 A regulation on reader target genes in specific context and it can be freely accessible at: https://github.com/NWPU-903PR/m6AexpressReader.
Bibliographic Details
http://www.sciencedirect.com/science/article/pii/S1046202322000755; http://dx.doi.org/10.1016/j.ymeth.2022.03.008; http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85127364023&origin=inward; http://www.ncbi.nlm.nih.gov/pubmed/35314342; https://linkinghub.elsevier.com/retrieve/pii/S1046202322000755; https://dx.doi.org/10.1016/j.ymeth.2022.03.008
Elsevier BV
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