ArticleGenome research2002
rVista for comparative sequence-based discovery of functional transcription factor binding sites.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 206 papers.
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Who cites it
206 citing papers in PubMed.
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- Oct4 cooperates with c-Myc to improve mesenchymal-to-endothelial transition and myocardial repair of cardiac-resident mesenchymal stem cells.Stem cell research & therapy · 2022Article
- Transcription factor GTF2B regulates AIP protein expression in growth hormone-secreting pituitary adenomas and influences tumor phenotypes.Neuro-oncology · 2022Article
- Aptamer-mediated transcriptional gene silencing ofMolecular therapy. Nucleic acids · 2021Article
- Comparison of machine learning and deep learning techniques in promoter prediction across diverse species.PeerJ. Computer science · 2021Article
- Transphyletic conservation of nitric oxide synthase regulation in cephalochordates and tunicates.Development genes and evolution · 2020Article
- Variation in the Promoter Region of theInternational journal of molecular sciences · 2019Article
- Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes.Cancer discovery · 2018Article
- Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis.BMC genomics · 2018Article
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- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Sonic hedgehog regulation ofDevelopment (Cambridge, England) · 2017Article
- Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression.BMC evolutionary biology · 2017Article
- SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells.Open biology · 2016Article
- Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton.PLoS genetics · 2016Article
- Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs.Scientific reports · 2016Article
- DNA demethylation of the TIM-3 promoter is critical for its stable expression on T cells.Genes and immunity · 2016Article
- Mutually repressive interaction between Brn1/2 and Rorb contributes to the establishment of neocortical layer 2/3 and layer 4.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
146 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVista, for high-throughput discovery of cis-regulatory elements that combines clustering of predicted transcription factor binding sites (TFBSs) and the analysis of interspecies sequence conservation to maximize the identification of functional sites. To assess the ability of rVista to discover true positive TFBSs while minimizing the prediction of false positives, we analyzed the distribution of several TFBSs across 1 Mb of the well-annotated cytokine gene cluster (Hs5q31; Mm11). Because a large number of AP-1, NFAT, and GATA-3 sites have been experimentally identified in this interval, we focused our analysis on the distribution of all binding sites specific for these transcription factors. The exploitation of the orthologous human-mouse dataset resulted in the elimination of > 95% of the approximately 58,000 binding sites predicted on analysis of the human sequence alone, whereas it identified 88% of the experimentally verified binding sites in this region.
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