Liu Chun-Chi, Lin Chin-Chung, Chen Wen-Shyen E, Chen Hsuan-Yu, Chang Pei-Chun, Chen Jeremy J W, Yang Pan-Chyr
Department of Computer Science, National Chung-Hsing University, Taichung, Taiwan, ROC.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W571-7. doi: 10.1093/nar/gkl279.
Transcription factors (TFs) and microRNAs play important roles in the regulation of human gene expression, and the study of their combinatory regulations of gene expression is a new research field. We constructed a comprehensive web server, the composite regulatory signature database (CRSD), that can be applied in investigating complex regulatory behaviors involving gene expression signatures (GESs), microRNA regulatory signatures (MRSs) and TF regulatory signatures (TRSs). Six well-known and large-scale databases, including the human UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway and Gene Ontology (GO) databases, were integrated to provide the comprehensive analysis in CRSD. Two new genome-wide databases, of MRSs and TRSs, were also constructed and further integrated into CRSD. To accomplish the microarray data analysis at one go, several methods, including microarray data pretreatment, statistical and clustering analysis, iterative enrichment analysis and motif discovery, were closely integrated in the web server, which has not been the case in previous studies. Our implementation showed that the published literature could demonstrate the results of genome-wide enrichment analysis. We conclude that CRSD is a powerful and useful bioinformatic web server and may provide new insights into gene regulation networks. CRSD and the online tutorial are publicly available at http://biochip.nchu.edu.tw/crsd1/.
转录因子（TFs）和微小RNA在人类基因表达调控中发挥着重要作用，对其基因表达组合调控的研究是一个新的研究领域。我们构建了一个综合性的网络服务器——复合调控特征数据库（CRSD），可用于研究涉及基因表达特征（GESs）、微小RNA调控特征（MRSs）和转录因子调控特征（TRSs）的复杂调控行为。整合了六个著名的大规模数据库，包括人类单基因数据库、成熟微小RNA数据库、假定启动子数据库、TRANSFAC数据库、通路数据库和基因本体（GO）数据库，以便在CRSD中进行综合分析。还构建了两个新的全基因组数据库，即MRSs数据库和TRSs数据库，并进一步整合到CRSD中。为了一次性完成微阵列数据分析，网络服务器中紧密集成了多种方法，包括微阵列数据预处理、统计和聚类分析、迭代富集分析和基序发现，而以往的研究并非如此。我们的实践表明，已发表的文献能够证明全基因组富集分析的结果。我们得出结论，CRSD是一个强大且有用的生物信息学网络服务器，可能为基因调控网络提供新的见解。CRSD及在线教程可在http://biochip.nchu.edu.tw/crsd1/上公开获取。
