ArticleJournal of integrative bioinformatics2022
A systematic study of motif pairs that may facilitate enhancer-promoter interactions.
Article in Journal of integrative 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, 4 citations in OpenAlex.
- DeepEPI: CNN-transformer-based model for extracting TF interactions through predicting enhancer-promoter interactions.Bioinformatics advances · 2025Article
- Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph.Frontiers in genetics · 2024Article
- A systematic study of HIF1A cofactors in hypoxic cancer cells.Scientific reports · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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Abstract
Pairs of interacting transcription factors (TFs) have previously been shown to bind to enhancers and promoters and contribute to their physical interactions. However, to date, we have limited knowledge about such TF pairs. To fill this void, we systematically studied the co-occurrence of TF-binding motifs in interacting enhancer-promoter (EP) pairs in seven human cell lines. We discovered 423 motif pairs that significantly co-occur in enhancers and promoters of interacting EP pairs. We demonstrated that these motif pairs are biologically meaningful and significantly enriched with motif pairs of known interacting TF pairs. We also showed that the identified motif pairs facilitated the discovery of the interacting EP pairs. The developed pipeline, EPmotifPair, together with the predicted motifs and motif pairs, is available at https://doi.org/10.6084/m9.figshare.14192000. Our study provides a comprehensive list of motif pairs that may contribute to EP physical interactions, which facilitate generating meaningful hypotheses for experimental validation.
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