ArticlePloS one2015
Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis.Computational and structural biotechnology journal · 2025Article
- Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development.Frontiers in immunology · 2023Article
- 3plex enables deep computational investigation of triplex forming lncRNAs.Computational and structural biotechnology journal · 2023Article
- Article
- Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana.Genome biology and evolution · 2021Article
- Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes.Nature genetics · 2020Article
- Exploring functionally annotated transcriptional consensus regulatory elements with CONREL.Database : the journal of biological databases and curation · 2020Article
- Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach.BMC bioinformatics · 2019Article
- Chromatin accessibility plays a key role in selective targeting of Hox proteins.Genome biology · 2019Article
- SP1 and STAT3 Functionally Synergize to Induce theCancers · 2019Article
- Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.NPJ genomic medicine · 2018Article
- A functional strategy to characterize expression Quantitative Trait Loci.Human genetics · 2017Article
- SOX5 is involved in balanced MITF regulation in human melanoma cells.BMC medical genomics · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors regulate gene expression by binding regulatory DNA. Understanding the rules governing such binding is an essential step in describing the network of regulatory interactions, and its pathological alterations. We show that describing regulatory regions in terms of their profile of total binding affinities for transcription factors leads to increased predictive power compared to methods based on the identification of discrete binding sites. This applies both to the prediction of transcription factor binding as revealed by ChIP-seq experiments and to the prediction of gene expression through RNA-seq. Further significant improvements in predictive power are obtained when regulatory regions are defined based on chromatin states inferred from histone modification data.
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