ArticleNucleic acids research2015
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- A systematic study of HIF1A cofactors in hypoxic cancer cells.Scientific reports · 2022Article
- A systematic study of motif pairs that may facilitate enhancer-promoter interactions.Journal of integrative bioinformatics · 2022Article
- Interpretation of deep learning in genomics and epigenomics.Briefings in bioinformatics · 2021Review
- An intriguing characteristic of enhancer-promoter interactions.BMC genomics · 2021Article
- Shared distal regulatory regions may contribute to the coordinated expression of human ribosomal protein genes.Genomics · 2020Article
- EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction.Bioinformatics (Oxford, England) · 2019Article
- Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.BMC genomics · 2019Article
- Integrative analyses shed new light on human ribosomal protein gene regulation.Scientific reports · 2016Article
- PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples.Database : the journal of biological databases and curation · 2015Article
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3 authors.
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Abstract
Comprehensive motif discovery under experimental conditions is critical for the global understanding of gene regulation. To generate a nearly complete list of human DNA motifs under given conditions, we employed a novel approach to de novo discover significant co-occurring DNA motifs in 349 human DNase I hypersensitive site datasets. We predicted 845 to 1325 motifs in each dataset, for a total of 2684 non-redundant motifs. These 2684 motifs contained 54.02 to 75.95% of the known motifs in seven large collections including TRANSFAC. In each dataset, we also discovered 43 663 to 2 013 288 motif modules, groups of motifs with their binding sites co-occurring in a significant number of short DNA regions. Compared with known interacting transcription factors in eight resources, the predicted motif modules on average included 84.23% of known interacting motifs. We further showed new features of the predicted motifs, such as motifs enriched in proximal regions rarely overlapped with motifs enriched in distal regions, motifs enriched in 5' distal regions were often enriched in 3' distal regions, etc. Finally, we observed that the 2684 predicted motifs classified the cell or tissue types of the datasets with an accuracy of 81.29%. The resources generated in this study are available at http://server.cs.ucf.edu/predrem/.
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