Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test

Lin Zhang, Jia Meng, Hui Liu, Xiaodong Cui, Shao Wu Zhang, Yidong Chen, Yufei Huang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

The study of mRNA methylation is an emerging research field greatly fueled by recent advancement in high throughput sequencing technology. We propose here a binomial likelihood ratio test ('bltest') aiming at detecting differentially methylated mRNA with MeRIP-Seq data, 'bltest' models the read counts of each RNA methylation site in IP and input samples with a binomial distribution. If the successful rates of binomial distributions under two experimental conditions are significantly different, the corresponding RNA is identified to be differentially methylated. The proposed 'bltest' does not require an independent procedure to unify different library sizes of the MeRIP-Seq samples, thus retaining maximal information from the data. Our simulation results clearly showed that 'bltest' consistently outperforms classic 'Fisher's exact test' at all settings. The proposed method was also applied to the real data, and the findings are consistent with previous studies.

Original languageEnglish (US)
Title of host publication2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1368-1371
Number of pages4
ISBN (Print)9781479970889
DOIs
StatePublished - Feb 5 2014
Event2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014 - Atlanta, United States
Duration: Dec 3 2014Dec 5 2014

Other

Other2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014
CountryUnited States
CityAtlanta
Period12/3/1412/5/14

Keywords

  • Binomial distribution
  • Differential RNA methylation
  • Likelihood ratio test
  • MA
  • MA-Seq
  • MeRIP-Seq
  • N6-Methyladenosine

ASJC Scopus subject areas

  • Signal Processing
  • Information Systems

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  • Cite this

    Zhang, L., Meng, J., Liu, H., Cui, X., Zhang, S. W., Chen, Y., & Huang, Y. (2014). Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test. In 2014 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2014 (pp. 1368-1371). [7032349] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/GlobalSIP.2014.7032349