ArticleNucleic acids research2013
PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Reannotation of cancer mutations based on expressed RNA transcripts reveals functional non-coding mutations in melanoma.American journal of human genetics · 2025Article
- Specific modulation of 28S_Um2402 rRNA 2'-NAR cancer · 2025Article
- Host-encoded CTCF regulates human cytomegalovirus latency via chromatin looping.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Identification of NAA40 as a Potential Prognostic Marker for Aggressive Liver Cancer Subtypes.Frontiers in oncology · 2021Article
- ECRG2, a novel transcriptional target of p53, modulates cancer cell sensitivity to DNA damage.Cell death & disease · 2020Article
- Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes.Frontiers in genetics · 2020Article
- Host signaling and EGR1 transcriptional control of human cytomegalovirus replication and latency.PLoS pathogens · 2019Article
- Insights into the transcriptional regulation of the anthracycline reductase AKR7A2 in human cardiomyocytes.Toxicology letters · 2019Article
- A novel method for improved accuracy of transcription factor binding site prediction.Nucleic acids research · 2018Article
- A proteomic analysis of an in vitro knock-out of miR-200c.Scientific reports · 2018Article
- Transcriptional interference by small transcripts in proximal promoter regions.Nucleic acids research · 2018Article
- Investigation of the role of DNA methylation in the expression of ERBB2 in human myocardium.Gene · 2017Article
- ConTra v3: a tool to identify transcription factor binding sites across species, update 2017.Nucleic acids research · 2017Article
- IGF2 mRNA binding protein 3 (IMP3) promotes glioma cell migration by enhancing the translation of RELA/p65.Oncotarget · 2017Article
- Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses.Scientific reports · 2017Article
- Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis.Advances and applications in bioinformatics and chemistry : AABC · 2017Article
- Article
- The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2.The Journal of experimental medicine · 2016Article
- Genetic characterisation of PPARG, CEBPA and RXRA, and their influence on meat quality traits in cattle.Journal of animal science and technology · 2016Article
- Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The most important mechanism in the regulation of transcription is the binding of a transcription factor (TF) to a DNA sequence called the TF binding site (TFBS). Most binding sites are short and degenerate, which makes predictions based on their primary sequence alone somewhat unreliable. We present a new web tool that implements a flexible and extensible algorithm for predicting TFBS. The algorithm makes use of both direct (the sequence) and several indirect readout features of protein-DNA complexes (biophysical properties such as bendability or the solvent-excluded surface of the DNA). This algorithm significantly outperforms state-of-the-art approaches for in silico identification of TFBS. Users can submit FASTA sequences for analysis in the PhysBinder integrative algorithm and choose from >60 different TF-binding models. The results of this analysis can be used to plan and steer wet-lab experiments. The PhysBinder web tool is freely available at http://bioit.dmbr.ugent.be/physbinder/index.php.
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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 OpenQuestion graph.