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Database Commons - SPD

SPD

Citations: 119

z-index 4.03

Short name SPD
Full name Secreted Protein Database
Description SPA, a collection of secreted proteins from Human, Mouse and Rat proteomes,is based on a bioinformatic pipeline and manual check, which includes sequences from SwissProt, Trembl, Ensembl and Refseq.
URL http://spd.cbi.pku.edu.cn
Year founded 2004
Last update & version 2006-07-06    v1.0
Availability Not Available
University/Institution hosted Peking University
Address Beijing 100871, China
City Beijing
Province/State
Country/Region China
Contact name Jingchu Luo
Contact email luojc@pku.edu.cn
Data type(s)
Major organism(s)
Keyword(s)
  • secreted proteins
Publication(s)
  • SPD--a web-based secreted protein database. [PMID: 15608170]

    Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, Jingchu Luo
    Nucleic acids research 2005:33(Database issue)
    119 Citations (Google Scholar as of 2016-01-22)

    Abstract: 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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Tags

Protein
Homo sapiens Mus musculus Rattus norvegicus
secreted proteins

Record metadata

  • Created on: 2015-07-11
  • Curated by:
    • Lin Xia [2016-03-28]
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