ArticleBMC bioinformatics2022
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed, 8 citations in OpenAlex.
- Article
- Databases and prospects of dynamic gene regulation in eukaryotes: A mini review.Computational and structural biotechnology journal · 2023Review
- CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events.BMC bioinformatics · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
motivationAberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor's motif.
resultsSEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease. AVAILABILITY AND IMPLEMENTATION: SEMplMe is available from https://github.com/Boyle-Lab/SEMplMe .
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