SynDB: a Synapse protein DataBase based on synapse ontology.
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.
Zhang
Wuxue
W
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences, Peking University, Beijing 100871, P.R. China.
Zhang
Yong
Y
Zheng
Hui
H
Zhang
Chen
C
Xiong
Wei
W
Olyarchuk
John G
JG
Walker
Michael
M
Xu
Weifeng
W
Zhao
Min
M
Zhao
Shuqi
S
Zhou
Zhuan
Z
Wei
Liping
L
D000818:Animals; D002874:Chromosome Mapping; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D051379:Mice; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D051381:Rats; D013569:Synapses / Q000502:physiology*; D014584:User-Computer Interface; D018875:Vocabulary, Controlled
D011506:Proteins