Ovcharenko Ivan, Nobrega Marcelo A
Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W403-7. doi: 10.1093/nar/gki466.
Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identifies synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in search of SREs and the results are displayed such as to provide an extensive annotation of the genes containing the detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. SynoR is publicly available at http://synor.dcode.org.
同义基因调控由驱动基因表达共享时空特征的调控元件所定义，极有可能基于包含某些转录因子结合位点（TFBS）相似模块的基因组元件。我们开发了一种方法，用于在脊椎动物基因组中扫描预定义配置下的TFBS进化保守模块，并创建了一个名为SynoR的工具，该工具可识别脊椎动物基因组中的同义调控元件（SRE）。SynoR利用活性调控元件（RE）中已知的TFBS模式作为基因组扫描的种子，从头识别SRE。多物种保守层允许在寻找SRE时使用差异系统发育序列保守过滤器，并展示结果以提供对包含检测到的RE的基因的广泛注释。利用基因本体类别对鉴定出的基因进行进一步功能分类，整合的GNF表达图谱2数据允许对预测的SRE的组织特异性进行编目。SynoR可在http://synor.dcode.org上公开获取。
