Institut für Genetik, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany.
Database (Oxford). 2010 Dec 21;2010:baq034. doi: 10.1093/database/baq034. Print 2010.
The AthaMap database generates a map of potential transcription factor binding sites (TFBS) and small RNA target sites in the Arabidopsis thaliana genome. The database contains sites for 115 different transcription factors (TFs). TFBS were identified with positional weight matrices (PWMs) or with single binding sites. With the new web tool 'Gene Identification', it is possible to identify potential target genes for selected TFs. For these analyses, the user can define a region of interest of up to 6000 bp in all annotated genes. For TFBS determined with PWMs, the search can be restricted to high-quality TFBS. The results are displayed in tables that identify the gene, position of the TFBS and, if applicable, individual score of the TFBS. In addition, data files can be downloaded that harbour positional information of TFBS of all TFs in a region between -2000 and +2000 bp relative to the transcription or translation start site. Also, data content of AthaMap was increased and the database was updated to the TAIR8 genome release. Database URL: http://www.athamap.de/gene_ident.php.
AthaMap 数据库生成了拟南芥基因组中潜在转录因子结合位点 (TFBS) 和小 RNA 靶位点的图谱。该数据库包含 115 种不同转录因子 (TF) 的位点。TFBS 是通过位置权重矩阵 (PWMs) 或单个结合位点来识别的。借助新的网络工具“Gene Identification”，可以识别选定 TF 的潜在靶基因。对于这些分析，用户可以在所有注释基因中定义一个最多达 6000bp 的感兴趣区域。对于使用 PWMs 确定的 TFBS，可以将搜索限制在高质量的 TFBS 上。结果以表格形式显示，其中标识基因、TFBS 的位置，如果适用，还有 TFBS 的单个分数。此外，还可以下载包含相对于转录或翻译起始位点在-2000 到+2000bp 范围内的所有 TF 的 TFBS 位置信息的数据文件。此外，还增加了 AthaMap 的数据库内容，并将数据库更新到了 TAIR8 基因组版本。数据库网址：http://www.athamap.de/gene_ident.php。
