EDGEdb:: a transcription factor-DNA Interaction database for the analysis of C-elegans differential gene expression
EDGEdb:: a transcription factor-DNA Interaction database for the analysis of C-elegans differential gene expression
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DOI：
10.1186/1471-2164-8-21
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发表时间：
2007-01-18
期刊：
影响因子：
4.4
通讯作者：
Walhout, Albertha J. M.
中科院分区：
文献类型：
--
作者：
Barrasa, M. Inmaculada;Vaglio, Philippe;Walhout, Albertha J. M.
背景：转录调控网络是由转录因子与其靶基因之间的蛋白质- dna相互作用组成的。基因组生物学的一个长期目标是绘制感兴趣的基因组中所有调控区域的蛋白质- dna相互作用网络。转录因子和以基因为中心的方法都可以用来系统地识别这种相互作用。我们使用高通量酵母单杂交实验作为一种以基因为中心的方法来鉴定秀丽隐杆线虫中调节序列（如基因启动子）和转录因子之间的蛋白质- dna相互作用。我们已经绘制了数百种蛋白质- dna相互作用的图谱，并通过检查在存在或不存在上游调节因子的情况下靶基因的差异表达，分析了一些蛋白质- dna相互作用的转录后果。在基因组尺度上，蛋白质- dna相互作用数据量的迅速增加需要一个数据库来促进有效的数据存储、检索和整合。描述：在这里，我们报告了秀丽隐杆线虫差异基因表达数据库（EDGEdb）的实现。该数据库能够存储和检索蛋白质- dna相互作用以及与差异基因表达相关的其他数据。具体来说，EDGEdb包含：i)调控元件的序列信息，包括基因启动子；ii)所有934个预测转录因子的序列信息，它们的DNA结合域，以及（如果有的话）它们的二聚化伙伴和一致的DNA结合位点；iii)调控元件和转录因子之间的蛋白质-DNA相互作用；iv)调控元件所带来的表达模式，以及这些模式如何受到相互作用的转录因子的影响。结论：EDGEdb为秀丽隐杆线虫转录因子提供了蛋白质- dna和蛋白质-蛋白质相互作用资源，并为其他生物的类似数据库提供了框架。该数据库可在http://edgedb.umassmed.edu上获得。
Background: Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-centered methods can be used to systematically identify such interactions. We use high-throughput yeast one-hybrid assays as a gene-centered method to identify protein-DNA interactions between regulatory sequences ( e. g. gene promoters) and transcription factors in the nematode Caenorhabditis elegans. We have already mapped several hundred protein-DNA interactions and analyzed the transcriptional consequences of some by examining differential gene expression of targets in the presence or absence of an upstream regulator. The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration.Description: Here, we report the implementation of a C. elegans differential gene expression database ( EDGEdb). This database enables the storage and retrieval of protein-DNA interactions and other data that relate to differential gene expression. Specifically, EDGEdb contains: i) sequence information of regulatory elements, including gene promoters, ii) sequence information of all 934 predicted transcription factors, their DNA binding domains, and, where available, their dimerization partners and consensus DNA binding sites, iii) protein-DNA interactions between regulatory elements and transcription factors, and iv) expression patterns conferred by regulatory elements, and how such patterns are affected by interacting transcription factors.Conclusion: EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms. The database is available at http://edgedb.umassmed.edu.