MethMotif Edit

Citations: 0

z-index: 0

Basic information
Short name MethMotif
Full name
Description a two-dimensional TFBS database that records TFBS position weight matrices along with cell type specific CpG methylation information computed from a combination of ChIP-seq and whole genome bisulfite sequencing datasets.
URL https://bioinfo-csi.nus.edu.sg/methmotif
Year founded 2018
Last update & version 2018
Availability Free to academic users only
Contact information
University/Institution hosted National University of Singapore
Address
City
Province/State
Country/Region Singapore
Contact name Touati Benoukraf
Contact email benoukraf@nus.edu.sg
Data information
Data object
  • Animal
Data type
  • DNA
Database category
  • Modification
Major organism
  • Homo sapiens
  • Mus musculus
Keyword
  • TF binding sites
  • DNA methylation
  • TFBS
Publications
  • MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. [PMID: 30380113]
    Quy Xiao Xuan Lin, Stephanie Sian, Omer An, Denis Thieffry, Sudhakar Jha, Touati Benoukraf

    Several recent studies have portrayed DNA methylation as a new player in the recruitment of transcription factors (TF) within chromatin, highlighting a need to connect TF binding sites (TFBS) with their respective DNA methylation profiles. However, current TFBS databases are restricted to DNA binding motif sequences. Here, we present MethMotif, a two-dimensional TFBS database that records TFBS position weight matrices along with cell type specific CpG methylation information computed from a combination of ChIP-seq and whole genome bisulfite sequencing datasets. Integrating TFBS motifs with TFBS DNA methylation better portrays the features of DNA loci recognised by TFs. In particular, we found that DNA methylation patterns within TFBS can be cell specific (e.g. MAFF). Furthermore, for a given TF, different DNA methylation profiles are associated with different DNA binding motifs (e.g. REST). To date, MethMotif database records overĀ 500 TFBSs computed from over 2000 ChIP-seq datasets in 11 different cell types. MethMotif portal is accessible through an open source web interface (https://bioinfo-csi.nus.edu.sg/methmotif) that allows users to intuitively explore the entire dataset and perform both single, and batch queries.

    Nucleic Acids Res. 2019:47(D1)

    0 Citations (from Europe PMC, 2019-01-19)

Word cloud

Tags

Record metadata

  • Created on: 2019-01-04
    • ***ina@***c.cn [2019-01-29]
    • ***ina@***c.cn [2019-01-29]
    • ***d@***c.cn [2019-01-12]
    • ***d@***c.cn [2019-01-12]
    • ***d@***c.cn [2019-01-04]

Community reviews 0 stars (0 reviews)

Data
quality & quantity
Content
organization & presentation
System
accessibility & reliability
Reviewed by