SynDB: a Synapse protein DataBase based on synapse ontology.

Wuxue Zhang; Yong Zhang; Hui Zheng; Chen Zhang; Wei Xiong; John G Olyarchuk; Michael Walker; Weifeng Xu; Min Zhao; Shuqi Zhao; Zhuan Zhou; Liping Wei

doi:10.1093/nar/gkl876

PubMed · 17098931

SynDB: a Synapse protein DataBase based on synapse ontology.

Wuxue Zhang·Yong Zhang·Hui Zheng·Chen Zhang·Wei Xiong·John G Olyarchuk·Michael Walker·Weifeng Xu·Min Zhao·Shuqi Zhao·Zhuan Zhou·Liping Wei

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Abstract

A synapse is the junction across which a nerve impulse passes from an axon terminal to a neuron, muscle cell or gland cell. The functions and building molecules of the synapse are essential to almost all neurobiological processes. To describe synaptic structures and functions, we have developed Synapse Ontology (SynO), a hierarchical representation that includes 177 terms with hundreds of synonyms and branches up to eight levels deep. associated 125 additional protein keywords and 109 InterPro domains with these SynO terms. Using a combination of automated keyword searches, domain searches and manual curation, we collected 14,000 non-redundant synapse-related proteins, including 3000 in human. We extensively annotated the proteins with information about sequence, structure, function, expression, pathways, interactions and disease associations and with hyperlinks to external databases. The data are stored and presented in the Synapse protein DataBase (SynDB, http://syndb.cbi.pku.edu.cn). SynDB can be interactively browsed by SynO, Gene Ontology (GO), domain families, species, chromosomal locations or Tribe-MCL clusters. It can also be searched by text (including Boolean operators) or by sequence similarity. SynDB is the most comprehensive database to date for synaptic proteins.

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Animals Chromosome Mapping Databases, Protein Humans Internet Mice Protein Structure, Tertiary Proteins Rats Synapses User-Computer Interface Vocabulary, Controlled Journal Article Research Support, Non-U.S. Gov't

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BibTeX RIS

Wuxue Zhang, Yong Zhang, Hui Zheng, Chen Zhang, Wei Xiong, John G Olyarchuk, Michael Walker, Weifeng Xu, Min Zhao, Shuqi Zhao, Zhuan Zhou, Liping Wei. 2006-11-10. SynDB: a Synapse protein DataBase based on synapse ontology.. https://doi.org/10.1093/nar%2Fgkl876

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