Integrated databases and computer systems for studying eukaryotic gene expression.
Integrated databases and computer systems for studying eukaryotic gene expression.
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用于研究真核基因表达的集成数据库和计算机系统。
DOI：
10.1093/bioinformatics/15.7.669
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发表时间：
1999
期刊：
影响因子：
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通讯作者：
Lavryushev,
中科院分区：
文献类型：
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作者：
Kolchanov,NA;Ponomarenko,MP;Frolov,AS;Ananko,EA;Kolpakov,FA;Ignatieva,EV;Podkolodnaya,OA;Goryachkovskaya,TN;Stepanenko,IL;Merkulova,TI;Babenko,VV;Ponomarenko,YV;Kochetov,AV;Podkolodny,NL;Vorobiev,DV;Lavryushev,
动机：这项工作的目标是开发一个面向WWW的计算机系统，提供最大限度地整合基因表达调控和导航方面的信息和软件资源。数据库中积累的关于基因表达调控的信息的种类和数量的快速增长必然要求开发用于自动发现可进一步用于分析调控基因组序列的知识的计算机系统。研究结果：GeneExpress系统包括以下主要信息模块和软件模块：（1）转录调控模块（TRRD），包含真核基因转录调控区数据库和TRRD Viewer，用于数据可视化;（2）位点活性预测模块（ACTIVITY），功能位点活性分析及其预测模块;（3）位点识别模块，其包括（a）B-DNA-VIDEO系统，用于检测对其识别重要的DNA位点的构象和物理化学性质，（B）共识和权重矩阵（c）转录因子结合位点识别（TFBSR）系统，用于检测功能位点的保守背景区域及其识别;（4）基因网络（GeneNet），它包含一个面向对象的数据库，积累了基因网络和信号转导途径的数据，以及基于Java的Viewer，用于探索和可视化GeneNet信息;（5）mRNA翻译（Leader mRNA），旨在分析mRNA 5 '-非翻译区（5'-UTR）的结构和背景特性，并预测其翻译效率;（6）其他研究调控基因组序列和调控蛋白的结构-功能组织的程序模块。可用性：基因表达可在http://wwwmgs.bionet.nsc。ru/systems/GeneExpress/，镜像站点的链接可在http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++找到。
MOTIVATION: The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. RESULTS: The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. AVAILABILITY: GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.