Comparative proteomics typically aims to systematically compare global protein expression profile between two cellular statuses (such as: disease and normal) and focuses on quantitative changes that occur as a function of disease, treatment or environment. Everyday, a wealth of experimental results about differentially expressed proteins (DEPs) are published and distribute among unformatted published literatures. Unfortunately, little effort has been taken to integrate them as unified data source and online database about DEPs is still unavailable. It obstructed scientists from getting reliable and valuable information of comparative proteomics rapidly.
DEPD, a relational database, was designed to store DEPs data from comparative proteomics experiments and provide a platform for data query and analysis. Till now, we have extracted more than 3,000 DEPs information from about 150 comparative proteomics references manually. These data were annotated reasonably with comprehensive information about biological, environmental and methodological contexts. To facilitate data query, submitting as well as communication between administrators and users, a user-friendly web interface was built. It also contains some tools for functional classification and pathway searching. You can find them in search/analysis pages. Additionally, a program named virtual 2D-Gel was created for DEPs' visualization. On the virtual 2D-Gel, DEPs are arrayed according to their theoretic pI score and molecular weight. Detail information about selected DEP can be shown in Protein Viewer page by clicking spots (DEPs) on virtual 2D-Gel.
CPXS 0.1(Comparative Proteomics XML Schema) is a new comparative proteomics minimum data standard which includes DEPs with some relevant context elements. As the purpose of CPXS 0.1 is not providing detail information for reproducing these experiments but highlighting correct biological meaning of DEPs, the most difficult and essential question is how to describe the complex context with a brief and flexible way. Detail reference can be found on CPXS page. If you have any suggestion please contact us .
The manuscript about DEPD has been accepted by bioinformatics and will be published soon. Please cite the reference: QuanYuan He, Jing Cao, XiangHua Liu, MiaoXin Li, YiSong Liu, JinYun Xie, SongPing Liang (2005) DEPD: a novel database for differentially expressed protein, Bioinformatics, 2005 Jul 14,in press.
We thank the authors of UniProt , BIND , KEGG and GO databases for data about protein function and pathway. This work was supported by a grant from National 973 Project of China (2001 CB510208), and a grant from National Natural Science Foundation of China (90408017).
If you encounter any problem, don't hesitate to contact us ( hqyone@hotmail.com ). We appreciate any suggestion and comment.
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