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用于分析和识别共调控基因的AthaMap网络工具。

AthaMap web tools for the analysis and identification of co-regulated genes.

作者信息

Galuschka Claudia, Schindler Martin, Bülow Lorenz, Hehl Reinhard

机构信息

Institut für Genetik, Technische Universität Braunschweig, Spielmanstrasse 7, D-38106 Braunschweig, Germany.

出版信息

Nucleic Acids Res. 2007 Jan;35(Database issue):D857-62. doi: 10.1093/nar/gkl1006. Epub 2006 Dec 5.

DOI:10.1093/nar/gkl1006
PMID:17148485
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1761422/
Abstract

The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at http://www.athamap.de/.

摘要

AthaMap数据库生成了拟南芥全基因组顺式调控元件图谱。该数据库通过新工具进行了扩展，以识别用户提供的基因集特定区域中的常见顺式调控元件。生成的表格显示了AthaMap中注释的所有顺式调控元件，包括相对于各自基因的位置信息。其他表格展示了各个转录因子结合位点（TFBS）的数量概况以及整个基因集共有的TFBS。过度表达的顺式元件很容易识别。这些特征被用于检测冷诱导基因中干旱响应元件的特异性富集。为了鉴定共调控基因，共定位功能的输出表格进行了扩展，以显示最接近的基因及其与共定位TFBS的相对距离。通过该功能确定的基因集可用于在诸如Genevestigator或PathoPlant等微阵列基因表达数据库中进行共调控分析。AthaMap的其他改进包括在序列窗口中显示基因结构以及显著增加数据量。可通过http://www.athamap.de/免费获取AthaMap。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1d0d/1781103/776b2318dce8/gkl1006f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1d0d/1781103/776b2318dce8/gkl1006f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1d0d/1781103/776b2318dce8/gkl1006f1.jpg

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