ArticleNucleic acids research2003
rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 30 citations in OpenAlex.
- A systematic, large-scale comparison of transcription factor binding site models.BMC genomics · 2016Article
- Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.BioMed research international · 2016Article
- rSNPBase: a database for curated regulatory SNPs.Nucleic acids research · 2014Article
- Identifying functional single nucleotide polymorphisms in the human CArGome.Physiological genomics · 2011Article
- Analytical methods for inferring functional effects of single base pair substitutions in human cancers.Human genetics · 2009Review
- SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.BMC bioinformatics · 2008Article
- Recent computational approaches to understand gene regulation: mining gene regulation in silico.Current genomics · 2007Article
- Identification of functional SNPs in the 5-prime flanking sequences of human genes.BMC genomics · 2005Article
- Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: the Human GPCR-DB Database.BMC genomics · 2004Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of gene regulatory networks has become one of the most challenging problems of the postgenomic era. Earlier we developed rSNP_Guide (http://util.bionet.nsc.ru/databases/rsnp.html), a computer system and database devoted to prediction of transcription factor (TF) binding sites (TF sites), which can be responsible for disease phenotypes. The prediction results were confirmed by 70 known relationships between TF sites and diseases, as well as by site-directed mutagenesis data. The rSNP_Guide is being investigated as a tool for TF site annotation. Previously analyzed and characterized cases of altered TF sites were used to annotate potential sites of the same type and at the same location in homologous genes. Based on 20 TF sites with known alterations in TF binding to DNA, we localized 245 potential TF sites in homologous genes. For these potential TF sites, rSNP_Guide estimates TF-DNA interaction according to three categories: 'present', 'weak', and 'absent'. The significance of each assignment is statistically measured.
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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 OpenQuestion graph.