ArticleNucleic acids research2014
TFBSshape: a motif database for DNA shape features of transcription factor binding sites.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions.Journal of molecular biology · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Mixing features of transcription factors and genes enable accurate prediction of gene regulation relationships for unknown transcription factors.NAR genomics and bioinformatics · 2026Article
- Genome-Wide Identification and Expression Profiling of Pyruvate Kinase Genes in Litchi Under Calcium-Magnesium Foliar Treatment.Plants (Basel, Switzerland) · 2025Article
- ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions.bioRxiv : the preprint server for biology · 2025Article
- CLAPE: Protein-Ligand Binding Site Prediction via Protein Language Models.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.Nucleic acids research · 2024Article
- CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells.Molecular oncology · 2023Article
- Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line.Life (Basel, Switzerland) · 2022Article
- JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.Nucleic acids research · 2022Article
- Diagnostic and therapeutic potential of RNASET2 in Crohn's disease: Disease-risk polymorphism modulates allelic-imbalance in expression and circulating protein levels and recombinant-RNASET2 attenuates pro-inflammatory cytokine secretion.Frontiers in immunology · 2022Article
- Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis.Frontiers in plant science · 2022Article
- Mechanisms of Binding Specificity among bHLH Transcription Factors.International journal of molecular sciences · 2021Review
- Targeting of eIF6-driven translation induces a metabolic rewiring that reduces NAFLD and the consequent evolution to hepatocellular carcinoma.Nature communications · 2021Article
- Article
- The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element.Biochemistry · 2020Article
- Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.Nucleic acids research · 2020Article
- Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins.Molecular cell · 2020Article
- TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.Nucleic acids research · 2020Article
- JASPAR 2020: update of the open-access database of transcription factor binding profiles.Nucleic acids research · 2020Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein-DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone.
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