TFBSshape


31665425	TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. [PMID: 31665425] Chiu TP, Xin B, Markarian N, Wang Y, Rohs R. 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. Nucleic Acids Res. 2020:48(D1) \| 22 Citations (from Europe PMC, 2025-03-22)
24214955	TFBSshape: a motif database for DNA shape features of transcription factor binding sites. [PMID: 24214955] Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R. 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. Nucleic Acids Res. 2014:42(Database issue) \| 78 Citations (from Europe PMC, 2025-03-22)

TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. [PMID: 31665425]

Chiu TP, Xin B, Markarian N, Wang Y, Rohs R.

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.

Nucleic Acids Res. 2020:48(D1) | 22 Citations (from Europe PMC, 2025-03-22)

TFBSshape: a motif database for DNA shape features of transcription factor binding sites. [PMID: 24214955]

Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R.

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.

Nucleic Acids Res. 2014:42(Database issue) | 78 Citations (from Europe PMC, 2025-03-22)

URL:	https://tfbsshape.usc.edu
Full name:	DNA shape features of transcription factor binding sites
Description:	a motif database for DNA shape features of transcription factor binding sites. 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.
Year founded:	2014
Last update:	2019-10-30
Version:	v2.0
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA
Data object:	Animal
Database category:	Structure
Major species:	Arabidopsis thaliana Caenorhabditis elegans Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus Zea mays Xenopus laevis Triticum aestivum Pisum sativum Petunia x hybrida Nicotiana spegazzinii
Keywords:	DNA structure transcription factor binding site shape-based alignment

University/Institution:	University of Southern California
Address:	Molecular and Computational Biology Program,University of Southern California,Los Angeles,CA 90089,USA
City:	Los Angeles
Province/State:	CA
Country/Region:	United States
Contact name (PI/Team):	Remo Rohs
Contact email (PI/Helpdesk):	rohs@usc.edu

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Database Commons a catalog of worldwide biological databases