Nucleic Acids Research: MeT-DB: a database of transcriptome methylation in mammalian cells

Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase (MeT-DB, http://compgenomics.utsa.edu/methylation/) is the first comprehensive resource for N6-methyladenosine (m⁶A) in the mammalian transcriptome. It includes a database that records publicly available data sets from methylated RNA immunoprecipitation sequencing (MeRIP-Seq), a recently developed technology for interrogating m⁶A methyltranscriptome. MeT-DB includes ∼300k m⁶A methylation sites in 74 MeRIP-Seq samples from 22 different experimental conditions predicted by exomePeak and MACS2 algorithms. To explore this rich information, MeT-DB also provides a genome browser to query and visualize context-specific m⁶A methylation under different conditions. MeT-DB also includes the binding site data of microRNA, splicing factor, and RNA binding proteins in the browser window for comparison with m⁶A sites and for exploring the potential functions of m⁶A. Analysis of differential m⁶A methylation and the related differential gene expression under two conditions is also available in the browser. A global perspective of the genome-wide distribution of m⁶A methylation in all the data is provided in circular ideograms, which also act as a navigation portal. The query results and the entire data set can be exported to assist publication and additional analysis.