Ponomarenko Julia V, Merkulova Tatyana I, Orlova Galina V, Fokin Oleg N, Gorshkova Elena V, Frolov Anatoly S, Valuev Vadim P, Ponomarenko Mikhail P
Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia.
Nucleic Acids Res. 2003 Jan 1;31(1):118-21. doi: 10.1093/nar/gkg112.
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.
基因调控网络分析已成为后基因组时代最具挑战性的问题之一。我们之前开发了rSNP_Guide（http://util.bionet.nsc.ru/databases/rsnp.html），这是一个致力于预测转录因子（TF）结合位点（TF位点）的计算机系统和数据库，这些位点可能与疾病表型有关。预测结果通过TF位点与疾病之间的70种已知关系以及定点诱变数据得到了证实。rSNP_Guide正作为一种TF位点注释工具进行研究。先前分析和表征的TF位点改变案例被用于注释同源基因中相同类型和相同位置的潜在位点。基于20个已知TF与DNA结合发生改变的TF位点，我们在同源基因中定位了245个潜在的TF位点。对于这些潜在的TF位点，rSNP_Guide根据“存在”“弱”和“不存在”三类来估计TF与DNA的相互作用。每次赋值的显著性都进行了统计学测量。
