MeT-DB: A database of transcriptome methylation in mammalian cells

Hui Liu; Mario A. Flores; Jia Meng; Lin Zhang; Xinyu Zhao; Manjeet K. Rao; Yidong Chen; Yufei Huang

doi:10.1093/nar/gku1024

MeT-DB: A database of transcriptome methylation in mammalian cells

Hui Liu, Mario A. Flores, Jia Meng, Lin Zhang, Xinyu Zhao, Manjeet K. Rao, Yidong Chen^*, Yufei Huang

^*Corresponding author for this work

Department of Biosciences and Bioinformatics

Research output: Contribution to journal › Article › peer-review

54 Citations (Scopus)

Abstract

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 mammalian transcriptome. It includes a database that records publicaly available data sets frommethylated 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 windowfor comparison withm⁶A sites and for exploring the potential functions of m⁶A. Analysis of differential m⁶Amethylation and the related differential gene expression under two conditions is also available in the browser. A global perspective of the genome-wide distribution ofm⁶A 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.

Original language	English
Pages (from-to)	D197-D203
Journal	Nucleic Acids Research
Volume	43
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gku1024
Publication status	Published - 28 Jan 2015

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title = "MeT-DB: A database of transcriptome methylation in mammalian cells",

abstract = "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 mammalian transcriptome. It includes a database that records publicaly available data sets frommethylated 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 windowfor comparison withm6A sites and for exploring the potential functions of m6A. Analysis of differential m6Amethylation and the related differential gene expression under two conditions is also available in the browser. A global perspective of the genome-wide distribution ofm6A 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.",

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MeT-DB: A database of transcriptome methylation in mammalian cells

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