AthaMap web tools for the analysis and identification of co-regulated genes.
AthaMap web tools for the analysis and identification of co-regulated genes.
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用于分析和识别共同调节基因的Athamap Web工具。
DOI：
10.1093/nar/gkl1006
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发表时间：
2007-01
影响因子：
14.9
通讯作者：
Hehl, Reinhard
中科院分区：
文献类型：
--
作者：
Galuschka, Claudia;Schindler, Martin;Buelow, Lorenz;Hehl, Reinhard
AthaMap数据库生成整个拟南芥基因组的顺式调控元件的图谱。这个数据库已经扩展了新的工具，以确定共同的顺式调控元件在特定区域的用户提供的基因集。所得表格显示了AthaMap中注释的所有顺式调控元件，包括相对于相应基因的位置信息。进一步的表格显示了存在的单个转录因子结合位点（TFBS）的数量和整个基因组共有的TFBS的概述。过量表达的顺式元件很容易识别。这些功能被用来检测特定的干旱响应元件在冷诱导基因的富集。为了鉴定共调节基因，共定位函数的输出表被扩展以显示最接近的基因及其与共定位TFBS的相对距离。由该函数确定的基因集可用于微阵列基因表达数据库如Genevestigator或PathoPlant中的共调控分析。AthaMap的其他改进包括在序列窗口中显示基因结构和显着的数据增加。AthaMap可在免费获得。
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 .
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影响因子：
5.4
作者：
Haas BJ;Wortman JR;Ronning CM;Hannick LI;Smith RK Jr;Maiti R;Chan AP;Yu C;Farzad M;Wu D;White O;Town CD
通讯作者：
Town CD
影响因子：
11.6
作者：
Huang, H;Tudor, M;Ma, H
通讯作者：
Ma, H
影响因子：
7.2
作者：
Gilmour, SJ;Zarka, DG;Thomashow, MF
通讯作者：
Thomashow, MF
影响因子：
4.9
作者：
Koshino-Kimura, Y;Wada, T;Okada, K
通讯作者：
Okada, K
影响因子：
14.9
作者：
Rhee, SY;Beavis, W;Zhang, PF
通讯作者：
Zhang, PF