Mockler T C, Michael T P, Priest H D, Shen R, Sullivan C M, Givan S A, McEntee C, Kay S A, Chory J
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.
Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.
The DIURNAL project ( http://diurnal.cgrb.oregonstate.edu/ ) provides a graphical interface for mining and viewing diurnal and circadian microarray data for Arabidopsis thaliana, poplar, and rice. The database is searchable and provides access to several user-friendly Web-based data-mining tools with easy-to-understand output. The associated tools include HAYSTACK ( http://haystack.cgrb.oregonstate.edu/ ) and ELEMENT ( http://element.cgrb.oregonstate.edu/ ). HAYSTACK is a model-based pattern-matching algorithm for identifying genes that are coexpressed and potentially coregulated. HAYSTACK can be used to analyze virtually any large-scale microarray data set and provides an alternative method for clustering microarray data from any experimental system by grouping together genes whose expression patterns match the same or similar user-defined patterns. ELEMENT is a Web-based program for identifying potential cis-regulatory elements in the promoters of coregulated genes in Arabidopsis, poplar, and rice. Together, DIURNAL, HAYSTACK, and ELEMENT can be used to facilitate cross-species comparisons among the plant species supported and to accelerate functional genomics efforts in the laboratory.
“昼夜节律”项目（http://diurnal.cgrb.oregonstate.edu/ ）提供了一个图形界面，用于挖掘和查看拟南芥、杨树和水稻的昼夜节律及生物钟微阵列数据。该数据库可进行搜索，并提供对几个用户友好的基于网络的数据挖掘工具的访问，输出结果易于理解。相关工具包括HAYSTACK（http://haystack.cgrb.oregonstate.edu/ ）和ELEMENT（http://element.cgrb.oregonstate.edu/ ）。HAYSTACK是一种基于模型的模式匹配算法，用于识别共表达且可能受到共同调控的基因。HAYSTACK几乎可用于分析任何大规模微阵列数据集，并通过将表达模式匹配相同或相似用户定义模式的基因分组，为聚类来自任何实验系统的微阵列数据提供了一种替代方法。ELEMENT是一个基于网络的程序，用于识别拟南芥、杨树和水稻中共同调控基因启动子中的潜在顺式调控元件。“昼夜节律”项目、HAYSTACK和ELEMENT一起可用于促进所支持植物物种之间的跨物种比较，并加速实验室中的功能基因组学研究工作。
