Nucleic Acids Research, 2005, Vol. 33, Database issue D169-D173
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
SPD—a web-based secreted protein database
Centre of Bioinformatics, College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China
* To whom correspondence should be addressed. Tel: +86 10 6275 7281; Fax: +86 10 6275 9001; Email: luojc{at}pku.edu.cn
Present address: Ying Jiang, Merck and Co. Inc., WP45-330, P.O. Box 4, West Point, PA 19486, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First authors
Received August 15, 2004; Revised and Accepted October 12, 2004
With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They were further annotated via a proteome annotation pipeline that we developed. We also set up a secreted protein classification pipeline and classified our predicted secreted proteins into different functional categories. To make the dataset more convincing and comprehensive, nine reference datasets are also integrated, such as the secreted proteins from the Gene Ontology Annotation (GOA) system at the European Bioinformatics Institute, and the vertebrate secreted proteins from Swiss-Prot. All these entries were grouped via a TribeMCL based clustering pipeline. We have constructed a web-based secreted protein database, which has been publicly available at http://spd.cbi.pku.edu.cn. Users can browse the database via a GO assignment or chromosomal-location-based interface. Moreover, text query and sequence similarity search are also provided, and the sequence and annotation data can be downloaded freely from the SPD website.
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