The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis

Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Arabidopsis / genetics
  • Arabidopsis / physiology
  • Circadian Rhythm / genetics*
  • Circadian Rhythm / physiology
  • DNA, Plant / genetics
  • Databases, Genetic*
  • Gene Expression Profiling / statistics & numerical data
  • Genes, Plant
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Oryza / genetics
  • Oryza / physiology
  • Pattern Recognition, Automated
  • Plant Physiological Phenomena
  • Plants / genetics*
  • Populus / genetics
  • Populus / physiology
  • Promoter Regions, Genetic
  • Regulatory Elements, Transcriptional
  • Software

Substances

  • DNA, Plant