Present address: Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA
Identification of putative plant cold responsive regulatory elements by gene expression profiling and a pattern enumeration algorithm
Article first published online: 1 SEP 2003
Plant Biotechnology Journal
Volume 1, Issue 5, pages 345–352, September 2003
How to Cite
Kreps, J., Budworth, P., Goff, S. and Wang, R. (2003), Identification of putative plant cold responsive regulatory elements by gene expression profiling and a pattern enumeration algorithm. Plant Biotechnology Journal, 1: 345–352. doi: 10.1046/j.1467-7652.2003.00032.x
- Issue published online: 1 SEP 2003
- Article first published online: 1 SEP 2003
- Received 25 March 2003; revised 19 May 2003; accepted 20 May 2003.
- cis elements search;
- expression profiling;
- whole genome bootstrapping
A pattern enumeration algorithm named GBSSR has been developed to analyse co-expressed gene groups identified through gene chip expression profiling to search for putative cis-regulatory elements, an important step toward understanding transcriptional factors, quantitative trait loci and gene regulatory networks. Without making any statistical assumptions, this algorithm establishes the frequency distribution of all eligible 6–15 bp strings by extensive bootstrap sampling from an entire genome worth of promoters, enabling those over-represented in a co-expressed gene group to be identified. Using a well-studied plant cold responsive gene system as a positive control, several known cold responsive elements were identified as top ranking candidates, along with some potentially novel ones. A typical analysis of 40 co-expressed genes takes a relatively inexpensive Linux cluster with 32 × 1.4 GHz Intel CPUs about 7 days to process.