The Diurnal Project: Diurnal and Circadian Expression Profiling, Model-based Pattern Matching, and Promoter Analysis
- T. C. Mockler*,
- T. P. Michael†,
- H. D. Priest*,
- R. Shen*,
- C. M. Sullivan*,
- S. A. Givan*,
- C. McEntee†,
- S. A. Kay‡, and
- J. Chory†§
- *Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- †Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
- ‡Department of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093-0116
- §Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037
Abstract
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.
Footnotes
- © Cold Spring Harbor Laboratory Press
