RARTF:: Database and tools for complete sets of Arabidopsis transcription factors
RARTF:: Database and tools for complete sets of Arabidopsis transcription factors
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DOI：
10.1093/dnares/dsi011
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发表时间：
2005-08-31
期刊：
影响因子：
4.1
通讯作者：
Shinozaki, Kazuo
中科院分区：
文献类型：
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作者：
Iida, Kei;Seki, Motoaki;Shinozaki, Kazuo
拟南芥基因组中超过5%的基因被认为是转录因子的编码基因。然而，很难准确识别它们。为了构建合适的转录因子集，我们使用PSI-BLAST和InterProScan，并手动检查了几个家族。特别是为了确定拟南芥的主要转录因子（MYB，AP 2/EREBP，bHLH，NAC，MADS，bZIP，WRKY），我们将PSI-BLAST搜索结果与最近的报道进行了比较。最后，我们确定了1968个蛋白质作为转录因子（所有拟南芥基因的7.4%）。基于所鉴定的转录因子，我们建立了名为RARTF（RIKEN Arabidopsis Transcription Factor database，http：//rarge.gsc.riken.jp/rartf/）的数据库。在RARTF中，我们提供了转录因子的功能基序，全长cDNA，选择性前mRNA剪接事件和Ac/Ds转座子标记的突变体的信息。我们还提供了400个转录因子基因在六个实验中的表达谱。我们将在不久的将来报道所有转录因子基因在各种胁迫和激素条件下在各种植物组织中的表达谱。
More than 5% of all genes in the Arabidopsis thaliana genome have been assumed to code for transcription factors. However, it has been difficult to accurately identify them. To construct proper sets of transcription factors, we used PSI-BLAST and InterProScan, and also checked several families manually. Especially to determine major Arabidopsis transcription factors (MYB, AP2/EREBP, bHLH, NAC, MADS, bZIP, WRKY), we compared the PSI-BLAST search results with those in recent reports. Finally, we identified 1968 proteins as transcription factors (7.4% of all Arabidopsis genes). We established a database named RARTF (RIKEN Arabidopsis Transcription Factor database, http://rarge.gsc.riken.jp/rartf/) based on the identified transcription factors. In RARTF, we provide information on the functional motif of transcription factors, full-length cDNAs, alternative pre-mRNA splicing events and Ac/Ds transposon-tagged mutants. We also provide expression profiles of 400 transcription factor genes in six experiments. We will report expression profiles of all transcription factor genes in various plant tissues under various stress and hormone conditions in the near future.