Introduction

Updated on September 26, 2014

Figure 1 Illustration of MeRIP-Seq experiment protocol.
    Figure 1. Illustration of MeRIP-Seq experiment     protocol

Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase (MeT-DB) is the first comprehensive resource for N6-methyladenosine (m6A) mammalian methyltranscriptome. It includes a database that records publically available datasets from methylated RNA immunoprecipitation sequencing (MeRIP-Seq)(Fig.1), a recently developed technology for interrogating m6A methyltranscriptome. All data are either aligned to UCSC/hg19 or UCSC/mm9 genome build, depending on the whether the samples are human or mouse, respectively. Each sample was evaluated by two peak detection algorithms: exomePeak and MACS2.

    Figure 2. Predicted m6A peaks by exomePeak and     MACS2 in MeT-DB

MeT-DB includes ~300k m6A methylation sites (detected by exomePeak, Fig.2) in 74 MeRIP-Seq samples from 22 (16 from human cells and 6 mouse cells) different experimental conditions. To explore this rich information, MeT-DB 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. Differential analysis of m6A methylation and custom-tracks for user uploadable methylation enrichment peaks are 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 of m6A sites and the entire datasets of predicted sites can be exported to assist publication and additional analysis.

Citing this website

Please cite MeT-DB by including the following reference in your manuscript:
Liu H, Flores MA, Meng J, Zhang L, Zhao X, Rao MK, Chen Y, Huang Y*. MeT-DB: a database of transcriptome methylation in mammalian cells. Nucleic Acids Res. 2014 Nov 6. pii: gku1024. PubMed PMID: 25378335.

For an extended list of publications where RNA methylation data are obtained, please see our Publications page.