The Database of cis-regulatory elements in Shewanella oneidensis is generated by comparative analysis of several Shewanella genomes in the recent Nucleic Acid Research publication of Xu, Liu and Stormo, 2008.
For genome-wide identification of cis-regulatory DNA sequence motifs in Shewanella, we applied a new comparative genomics approach that combines phylogenetic footprinting, motif searching, and motif clustering approaches to predict novel DNA motifs that are not only conserved across species but also shared by multiple genes. A large number of our predictions match known motifs or are supported by literature or other independent evidence such as functional enrichment and expression coherence of the genes sharing the same motifs, suggesting that many of these predictions are correct. In addition, we applied the pipeline to differentially expressed genes from microarray experiments and identified DNA motifs specifically involved in metal reduction. This study provides one of the most comprehensive transcriptional regulatory networks in bacterial genomes.
To better serve the Shewanella research community, we not only provide the "Browse" page to serve as the supplementary materials for the NAR publication, but also provide two "Search" functions that allow users to retrieve useful information by gene or by motif profile, respectively.
If information in the supplementary material is used in work that is published, please cite:
Xing Xu*, Jiajian Liu*, and Gary D. Stormo
The cis-regulatory map of Shewanella genomes
Nucleic Acids Research, 36(16):5376-5390, August 2008;
* Equally contributed.
We are very excited about the fact that a large number of our predictions are supported by independent evidence and provide promising candidates for experimental validation. If you think some of motifs are interesting and want to explore them further, collaborations are always very welcome. Please contact us.
© 2008 Xing Xu, Jiajian Liu and Gary Stormo, Washington University School of Medicine.