m6Acorr: an online tool for the correction and comparison of m(6)A methylation profiles

BACKGROUND: The analysis and comparison of RNA m(6)A methylation profiles have become increasingly important for understanding the post-transcriptional regulations of gene expression. However, current m(6)A profiles in public databases are not readily intercomparable, where heterogeneous profiles from the same experimental report but different cell types showed unwanted high correlations. RESULTS: Several normalizing or correcting methods were tested to remove such laboratory bias. And m6Acorr, an effective pipeline for correcting m(6)A profiles, was presented on the basis of quantile normalization and empirical Bayes batch regression method. m6Acorr could efficiently correct laboratory bias in the simulated dataset and real m(6)A profiles in public databases. The preservation of biological signals was examined after correction, and m6Acorr was found to better preserve differential methylation signals, m(6)A regulated targets, and m(6)A-related biological features than alternative methods. Finally, the m6Acorr server was established. This server could eliminate the potential laboratory bias in m(6)A methylation profiles and perform profile–profile comparisons and functional analysis of hyper- (hypo-) methylated genes based on corrected methylation profiles. CONCLUSION: m6Acorr was established to correct the existing laboratory bias in RNA m(6)A methylation profiles and perform profile comparisons on the corrected datasets. The m6Acorr server is available at http://www.rnanut.net/m6Acorr. A stand-alone version with the correction function is also available in GitHub at https://github.com/emersON106/m6Acorr.