Identification of putative plant cold responsive regulatory elements by gene expression profiling and a pattern enumeration algorithm.

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 x 1.4 GHz Intel CPUs about 7 days to process.