ArticleNucleic acids research2019
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 93 citations in OpenAlex.
- Second-order threat conditioning in the amygdala-posterior piriform cortex network.Communications biology · 2025Article
- Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive Transcription Factors.Current protocols · 2025Article
- Article
- DNA Methylation in the CYP3A Distal Regulatory Region (DRR) Is Associated with the Expression of CYP3A5 and CYP3A7 in Human Liver Samples.Molecules (Basel, Switzerland) · 2024Article
- MethylSeqLogo: DNA methylation smart sequence logos.BMC bioinformatics · 2024Article
- Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors.Acta neuropathologica communications · 2024Article
- CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer.Database : the journal of biological databases and curation · 2024Article
- Less-is-more: selecting transcription factor binding regions informative for motif inference.Nucleic acids research · 2024Article
- Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation.Clinical epigenetics · 2024Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.Nucleic acids research · 2024Article
- MethMotif.Org 2024: a database integrating context-specific transcription factor-binding motifs with DNA methylation patterns.Nucleic acids research · 2024Article
- The role of epigenetics in women's reproductive health: the impact of environmental factors.Frontiers in endocrinology · 2024Review
- Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.Nucleic acids research · 2023Article
- DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer.Clinical epigenetics · 2023Article
- The Interplay between Dysregulated Metabolism and Epigenetics in Cancer.Biomolecules · 2023Review
- Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes.Nature communications · 2023Article
- CanMethdb: a database for genome-wide DNA methylation annotation in cancers.Bioinformatics (Oxford, England) · 2023Article
- Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38.Epigenetics · 2022Article
- SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.BMC bioinformatics · 2022Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 over 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.