TDTHub, a web server tool for the analysis of transcription factor binding sites in plants.
TDTHub, a web server tool for the analysis of transcription factor binding sites in plants.
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TDTHub，一个用于分析植物转录因子结合位点的web服务器工具。
DOI：
10.1111/tpj.15873
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发表时间：
2022-08
期刊：
影响因子：
7.2
通讯作者：
Franco-Zorrilla, Jose M.
中科院分区：
文献类型：
--
作者：
Grau, Joaquin;Franco-Zorrilla, Jose M.
关键词：
转录调控是植物对环境变化的大多数发育程序和生理反应的基础。转录因子通过与基因调控区域的短DNA序列--转录因子结合位点(TFBs)特异性结合，在基因表达调控中发挥关键作用。近年来，已经开发了几种生物信息学工具来检测候选基因中的TFBS，要么通过从头预测，要么通过直接定位实验已知的TFBS。然而，这些工具中的大多数只包含少数物种的信息，或者需要多个步骤，对于没有经验的研究人员来说并不总是直观的。在这里，我们介绍了TFBS-发现工具中心(TDTHub)，这是一个用于快速和直观地研究植物转录调控的网络服务器。TDTHub在40种植物中使用了预先计算的TFBS，并允许选择两种映射算法，提供了更高的通用性。除了主要的TFBS丰富工具外，TDTHub还包括其他工具来帮助分析和可视化数据。为了证明TDTHub的有效性，我们分析了花青素生物合成途径的转录调控。我们还分析了茉莉酸和伤害分别在拟南芥和番茄(Solanum Lycopsicum)中的转录级联反应。在这些研究中，TDTHub帮助验证了最相关的TF节点，并提出了在这些通路中具有突出作用的新节点。TDTHub可在http://acrab.cnb.csic.es/TDTHub/，上获得，它将定期升级和扩展，以适应新物种和基因注释。转录因子(Tf)是通过识别同源DNA基序，即转录因子结合位点(TFBs)调控基因表达的主要因子。大多数检测TFBS的生物信息学工具仅限于少数物种，或者需要多个步骤。我们介绍了TDTHub，一个用于快速和直观地研究植物转录调控的网络服务器。TDTHub在40个物种中使用了预先计算的TFBSS，并包括其他工具来帮助分析和可视化数据。
Transcriptional regulation underlies most developmental programs and physiological responses to environmental changes in plants. Transcription factors (TFs) play a key role in the regulation of gene expression by binding specifically to short DNA sequences in the regulatory regions of genes: the TF binding sites (TFBSs). In recent years, several bioinformatic tools have been developed to detect TFBSs in candidate genes, either by de novo prediction or by directly mapping experimentally known TFBSs. However, most of these tools contain information for only a few species or require multi‐step procedures, and are not always intuitive for non‐experienced researchers. Here we present TFBS‐Discovery Tool Hub (TDTHub), a web server for quick and intuitive studies of transcriptional regulation in plants. TDTHub uses pre‐computed TFBSs in 40 plant species and allows the choice of two mapping algorithms, providing a higher versatility. Besides the main TFBS enrichment tool, TDTHub includes additional tools to assist in the analysis and visualization of data. In order to demonstrate the effectiveness of TDTHub, we analyzed the transcriptional regulation of the anthocyanin biosynthesis pathway. We also analyzed the transcriptional cascades in response to jasmonate and wounding in Arabidopsis and tomato (Solanum lycopersicum), respectively. In these studies, TDTHub helped to verify the most relevant TF nodes and to propose new ones with a prominent role in these pathways. TDTHub is available at http://acrab.cnb.csic.es/TDTHub/, and it will be periodically upgraded and expanded for new species and gene annotations. Transcription factors (TFs) are the main players during regulation of gene expression through recognition of cognate DNA motifs, the TF binding sites (TFBSs). Most bioinformatic tools to detect TFBSs are restricted to only a few species or require multi‐step procedures. We present TDTHub, a web server for quick and intuitive studies of transcriptional regulation in plants. TDTHub uses pre‐computed TFBSs in 40 species and includes additional tools to help in the analysis and visualization of data.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
DOI：
10.1073/pnas.1316278111
发表时间：
2014-02-11
影响因子：
11.1
作者：
Franco-Zorrilla, Jose M.;Lopez-Vidriero, Irene;Solano, Roberto
通讯作者：
Solano, Roberto
影响因子：
3.7
作者：
Gearing, Linden J.;Cumming, Helen E.;Hertzog, Paul J.
通讯作者：
Hertzog, Paul J.
AthaMap，整合转录和转录后数据。
影响因子：
14.9
作者：
Buelow, Lorenz;Engelmann, Stefan;Schindler, Martin;Hehl, Reinhard
通讯作者：
Hehl, Reinhard
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS