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

Nucleic Acids Res. 2015 Jan;43(Database issue):D197-203. doi: 10.1093/nar/gku1024. Epub 2014 Nov 6.

Authors

Hui Liu¹, Mario A Flores², Jia Meng³, Lin Zhang¹, Xinyu Zhao⁴, Manjeet K Rao⁵, Yidong Chen⁶, Yufei Huang⁷

Affiliations

¹ School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China.
² Department of Electrical and Computer Engineering, University of Texas at San Antonio, TX 78249-0669, USA.
³ Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.
⁴ Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX 78229, USA.
⁵ Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX 78229, USA Department of Cellular Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA.
⁶ Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX 78229, USA Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, TX 78229, USA yufei.huang@utsa.edu.
⁷ Department of Electrical and Computer Engineering, University of Texas at San Antonio, TX 78249-0669, USA Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, TX 78229, USA ChenY8@uthscsa.edu.

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 (m(6)A) in mammalian transcriptome. It includes a database that records publicaly available data sets from methylated RNA immunoprecipitation sequencing (MeRIP-Seq), a recently developed technology for interrogating m(6)A methyltranscriptome. MeT-DB includes ∼ 300 k m(6)A 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 m(6)A 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 m(6)A sites and for exploring the potential functions of m(6)A. Analysis of differential m(6)A 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 m(6)A 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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adenosine / analogs & derivatives*
Adenosine / metabolism
Animals
Binding Sites
Databases, Nucleic Acid*
Gene Expression Profiling / methods*
Humans
Immunoprecipitation
Methylation
Mice
MicroRNAs / metabolism
RNA, Messenger / metabolism*
RNA-Binding Proteins / metabolism
Sequence Analysis, RNA

Substances

MicroRNAs
RNA, Messenger
RNA-Binding Proteins
N-methyladenosine
Adenosine

Abstract

Publication types

MeSH terms

Substances

Grants and funding