Differential RNA methylation using multivariate statistical methods.
Brief Bioinform
; 23(1)2022 01 17.
Article
in En
| MEDLINE
| ID: mdl-34586372
ABSTRACT
MOTIVATION m6A methylation is a highly prevalent post-transcriptional modification in eukaryotes. MeRIP-seq or m6A-seq, which comprises immunoprecipitation of methylation fragments , is the most common method for measuring methylation signals. Existing computational tools for analyzing MeRIP-seq data sets and identifying differentially methylated genes/regions are not most optimal. They either ignore the sparsity or dependence structure of the methylation signals within a gene/region. Modeling the methylation signals using univariate distributions could also lead to high type I error rates and low sensitivity. In this paper, we propose using mean vector testing (MVT) procedures for testing differential methylation of RNA at the gene level. MVTs use a distribution-free test statistic with proven ability to control type I error even for extremely small sample sizes. We performed a comprehensive simulation study comparing the MVTs to existing MeRIP-seq data analysis tools. Comparative analysis of existing MeRIP-seq data sets is presented to illustrate the advantage of using MVTs. RESULTS:
Mean vector testing procedures are observed to control type I error rate and achieve high power for detecting differential RNA methylation using m6A-seq data. Results from two data sets indicate that the genes detected identified as having different m6A methylation patterns have high functional relevance to the study conditions.AVAILABILITY:
The dimer software package for differential RNA methylation analysis is freely available at https//github.com/ouyang-lab/DIMER. SUPPLEMENTARY INFORMATION Supplementary data are available at Briefings in Bioinformatics online.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
RNA
Language:
En
Journal:
Brief Bioinform
Journal subject:
BIOLOGIA
/
INFORMATICA MEDICA
Year:
2022
Document type:
Article
Affiliation country:
Estados Unidos