RSNP_Guide, a Database System for Analysis of Transcription Factor Binding to DNA with Variations: Application to Genome Annotation

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Jan 10

PMID 12519962

Citations 9

Authors

Julia V Ponomarenko

Tatyana I Merkulova

Galina V Orlova

Oleg N Fokin

Elena V Gorshkova

Anatoly S Frolov

Vadim P Valuev

Mikhail P Ponomarenko

Affiliations

Soon will be listed here.

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.

Citing Articles

Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.

Ponomarenko P, Rasskazov D, Suslov V, Sharypova E, Savinkova L, Podkolodnaya O Biomed Res Int. 2016; 2016:8642703.

PMID: 27635400 PMC: 5011241. DOI: 10.1155/2016/8642703.

A systematic, large-scale comparison of transcription factor binding site models.

Hombach D, Schwarz J, Robinson P, Schuelke M, Seelow D BMC Genomics. 2016; 17:388.

PMID: 27209209 PMC: 4875604. DOI: 10.1186/s12864-016-2729-8.

rSNPBase: a database for curated regulatory SNPs.

Guo L, Du Y, Chang S, Zhang K, Wang J Nucleic Acids Res. 2013; 42(Database issue):D1033-9.

PMID: 24285297 PMC: 3964952. DOI: 10.1093/nar/gkt1167.

Identifying functional single nucleotide polymorphisms in the human CArGome.

Benson C, Zhou Q, Long X, Miano J Physiol Genomics. 2011; 43(18):1038-48.

PMID: 21771879 PMC: 3180741. DOI: 10.1152/physiolgenomics.00098.2011.

Analytical methods for inferring functional effects of single base pair substitutions in human cancers.

Lee W, Yue P, Zhang Z Hum Genet. 2009; 126(4):481-98.

PMID: 19434427 PMC: 2762536. DOI: 10.1007/s00439-009-0677-y.

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