ArticleNucleic acids research2020
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Identification and evaluation of 41 risk loci for juvenile idiopathic arthritis informs precision medicine: mechanistic implications of DNA topology and an HLA-A*02:01-ERAP2 interaction.medRxiv : the preprint server for health sciences · 2026Article
- ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions.Journal of molecular biology · 2026Article
- RNA Pol I shapes meiotic chromatin, germline H3K4me3 dynamics, and oogenesis independent of ribosome assembly.Cell reports · 2026Article
- Gene regulatory network inference with popInfer reveals the dynamic regulation of hematopoietic stem cell quiescence.iScience · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis.bioRxiv : the preprint server for biology · 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
- Article
- Motif distribution in genomes gives insights into gene clustering and co-regulation.Nucleic acids research · 2025Article
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum.Nucleic acids research · 2024Article
- Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.Nucleic acids research · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- Harnessing regulatory networks in Actinobacteria for natural product discovery.Journal of industrial microbiology & biotechnology · 2024Review
- JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.Nucleic acids research · 2022Article
- Towards rational computational peptide design.Frontiers in bioinformatics · 2022Article
- Host-pathogen protein-nucleic acid interactions: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- Local DNA shape is a general principle of transcription factor binding specificity in Arabidopsis thaliana.Nature communications · 2021Article
- Predicting transcription factor binding sites using DNA shape features based on shared hybrid deep learning architecture.Molecular therapy. Nucleic acids · 2021Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
TFBSshape (https://tfbsshape.usc.edu) is a motif database for analyzing structural profiles of transcription factor binding sites (TFBSs). The main rationale for this database is to be able to derive mechanistic insights in protein-DNA readout modes from sequencing data without available structures. We extended the quantity and dimensionality of TFBSshape, from mostly in vitro to in vivo binding and from unmethylated to methylated DNA. This new release of TFBSshape improves its functionality and launches a responsive and user-friendly web interface for easy access to the data. The current expansion includes new entries from the most recent collections of transcription factors (TFs) from the JASPAR and UniPROBE databases, methylated TFBSs derived from in vitro high-throughput EpiSELEX-seq binding assays and in vivo methylated TFBSs from the MeDReaders database. TFBSshape content has increased to 2428 structural profiles for 1900 TFs from 39 different species. The structural profiles for each TFBS entry now include 13 shape features and minor groove electrostatic potential for standard DNA and four shape features for methylated DNA. We improved the flexibility and accuracy for the shape-based alignment of TFBSs and designed new tools to compare methylated and unmethylated structural profiles of TFs and methods to derive DNA shape-preserving nucleotide mutations in TFBSs.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.