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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 227.
Published online May 16, 2009. doi:  10.1186/1471-2164-10-227
PMCID: PMC2690602
plantsUPS: a database of plants' Ubiquitin Proteasome System
Zhou Du,1 Xin Zhou,1 Li Li,1 and Zhen Sucorresponding author1
1State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
corresponding authorCorresponding author.
Zhou Du: adugduzhou/at/gmail.com; Xin Zhou: xzhou82/at/gmail.com; Li Li: walkcoolboyli/at/gmail.com; Zhen Su: zhensu/at/cau.edu.cn
Received March 21, 2009; Accepted May 16, 2009.
Abstract
Background
The ubiquitin 26S/proteasome system (UPS), a serial cascade process of protein ubiquitination and degradation, is the last step for most cellular proteins. There are many genes involved in this system, but are not identified in many species. The accumulating availability of genomic sequence data is generating more demands in data management and analysis. Genomics data of plants such as Populus trichocarpa, Medicago truncatula, Glycine max and others are now publicly accessible. It is time to integrate information on classes of genes for complex protein systems such as UPS.
Results
We developed a database of higher plants' UPS, named 'plantsUPS'. Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.
Conclusion
The plantsUPS enables the exploration and comparative analysis of UPS in higher plants. It now archives > 8000 genes from seven plant species distributed in 11 UPS-involved gene families. The plantsUPS is freely available now to all users at http://bioinformatics.cau.edu.cn/plantsUPS.
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