Identification of putative plant cold responsive regulatory elements by gene expression profiling and a pattern enumeration algorithm
Joel Kreps
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
These authors are equal contributors. Present address: Diversa Corporation, 4955 Directors Place, San Diego, CA 92121-1609, USA
Search for more papers by this authorPaul Budworth
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
These authors are equal contributors. Present address: Diversa Corporation, 4955 Directors Place, San Diego, CA 92121-1609, USA
Search for more papers by this authorSteve Goff
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
Present address: Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA
Search for more papers by this authorCorresponding Author
Ronglin Wang
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
Present address: Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA
Correspondence (tel +1 919 765 5114; fax +1 919 541 8557; e-mail [email protected])Search for more papers by this authorJoel Kreps
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
These authors are equal contributors. Present address: Diversa Corporation, 4955 Directors Place, San Diego, CA 92121-1609, USA
Search for more papers by this authorPaul Budworth
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
These authors are equal contributors. Present address: Diversa Corporation, 4955 Directors Place, San Diego, CA 92121-1609, USA
Search for more papers by this authorSteve Goff
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
Present address: Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA
Search for more papers by this authorCorresponding Author
Ronglin Wang
Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
Present address: Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA
Correspondence (tel +1 919 765 5114; fax +1 919 541 8557; e-mail [email protected])Search for more papers by this authorSummary
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.
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