The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
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.
Mockler
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TC
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.
Michael
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TP
Priest
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HD
Shen
R
R
Sullivan
C M
CM
Givan
S A
SA
McEntee
C
C
Kay
S A
SA
Chory
J
J
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics / Q000502:physiology; D002940:Circadian Rhythm / Q000235:genetics* / Q000502:physiology; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D017343:Genes, Plant; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D012275:Oryza / Q000235:genetics / Q000502:physiology; D010363:Pattern Recognition, Automated; D018521:Plant Physiological Phenomena; D010944:Plants / Q000235:genetics*; D032107:Populus / Q000235:genetics / Q000502:physiology; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D012984:Software
D018744:DNA, Plant