ArticleNucleic acids research2017
ConTra v3: a tool to identify transcription factor binding sites across species, update 2017.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- KCTD15 deregulation is associated with alterations of the NF-κB signaling in both pathological and physiological model systems.Scientific reports · 2021Trial
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- SGK3 promoter deletion in late-onset hypophosphatemic rickets, a possible genetic cause of the disease.Orphanet journal of rare diseases · 2026Article
- Curcumin pretreatment enhances the capacity of BMSC exosomes to attenuate renal ischemia-reperfusion injury by ferroptosis suppression via miR-16-5p/Smad3/Mb axis.Stem cell research & therapy · 2026Article
- Creatine kinase B, a downstream effector of c-Myb, controls migration of osteosarcoma cells via regulation of N-cadherin.Cancer cell international · 2025Article
- NFATc1 drives Orai3 transcription and proteolysis by harnessing epigenome differences in the MARCH8 promoter.The EMBO journal · 2025Article
- Unraveling the functional dynamics of Caenorhabditis elegans stress-responsive omega class GST-44.The FEBS journal · 2025Article
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- GD3 synthase drives resistance to p53-induced apoptosis in breast cancer by modulating mitochondrial function.Oncogene · 2025Article
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- Integrated multi-omics analysis and functional validation uncovers RPL26 roles in regulating growth traits of Asian water buffaloes (Bubalus bubalis).BMC genomics · 2025Article
- NF-κB-mediated EAAT3 upregulation in antioxidant defense and ferroptosis sensitivity in lung cancer.Cell death & disease · 2025Article
- Glycogen synthase is required for heat shock-mediated autophagy induction in neuronal cells.Biology open · 2025Article
- Cold atmospheric plasma potentiates ferroptosis via EGFR(Y1068)-mediated dual axes on GPX4 among triple negative breast cancer cells.International journal of biological sciences · 2025Article
- The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes.BMC bioinformatics · 2024Article
- Mitochondrial calcium uptake orchestrates vertebrate pigmentation via transcriptional regulation of keratin filaments.PLoS biology · 2024Article
- Osteomodulin deficiency in mice causes a specific reduction of transversal cortical bone size.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2024Article
- Involvement of Kindlin-1 in cutaneous squamous cell carcinoma.Oncogenesis · 2024Article
- Sialic Acid-Siglec-E Interactions Regulate the Response of Neonatal Macrophages to Group B Streptococcus.ImmunoHorizons · 2024Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region surrounding coding or non-coding genes. In this updated version, with a completely re-implemented user interface using latest web technologies, users can choose from nine reference organisms ranging from human to yeast. ConTra v3 can analyze promoter regions, 5΄-UTRs, 3΄-UTRs and introns or any other genomic region of interest. Thousands of position weight matrices are available to choose from for detecting specific binding sites. Besides this visualization option, additional new exploration functionality is added to the tool that will automatically detect TFBSs having at the same time the highest regulatory potential, the highest conservation scores of the genomic regions covered by the predicted TFBSs and strongest co-localizations with genomic regions exhibiting regulatory activity. The ConTra v3 web server is freely available at http://bioit2.irc.ugent.be/contra/v3.
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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.