| Autor: |
Joel, Kreps, Paul, Budworth, Steve, Goff, Ronglin, Wang |
| Rok vydání: |
2006 |
| Zdroj: |
Plant biotechnology journal. 1(5) |
| ISSN: |
1467-7652 |
| Popis: |
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. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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