Paper Info
Title
rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation.
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.bione.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.
Year
DOI
Venue
2003
10.1093/nar/gkg112
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
genomics,dna binding proteins,dna,gene regulatory network,genome,binding sites,gene expression regulation,database system,site directed mutagenesis,genome annotation,binding site,transcription factor,transcription factors,computational biology
Genome,Binding site,Gene,Genome project,Biology,DNA-binding protein,Genomics,Genetics,Gene regulatory network,Molecular biology,Database,Transcription factor
Journal
Volume
Issue
ISSN
31
1
0305-1048
Citations 
PageRank 
References 
5
0.62
7
Authors
8
Name
Order
Citations
PageRank
Julia V. Ponomarenko125724.02
Tatyana I. Merkulova211412.70
Galina Orlova3387.54
Oleg N. Fokin4183.19
Elena Gorshkova5112.35
Anatoly S. Frolov610015.56
Vadim P. Valuev7121.75
Mikhail P Ponomarenko813127.97