4.8 Article

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

期刊

NUCLEIC ACIDS RESEARCH
卷 43, 期 D1, 页码 D197-D203

出版社

OXFORD UNIV PRESS
DOI: 10.1093/nar/gku1024

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资金

  1. National Institutes of Health [NIH-NCIP30CA54174, R01GM113245]
  2. National Science Foundation [CCF-1246073]
  3. National Natural Science Foundation of China [61201408, 61401370]
  4. China Fundamental Research Funds for the Central Universities [2014QNA84, 2014QNB47]
  5. Jiangsu Natural Science Foundation [BK20140403]
  6. Greehey Children's Cancer Research Institute's summer internship
  7. Direct For Computer & Info Scie & Enginr
  8. Division of Computing and Communication Foundations [1246073] Funding Source: National Science Foundation

向作者/读者索取更多资源

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 similar to 300k 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.

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