Nucleic Acids Research Advance Access originally published online on November 29, 2006
Nucleic Acids Research 2007 35(Database issue):D538-D545; doi:10.1093/nar/gkl937
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Nucleic Acids Research, 2007, Vol. 35, Database issue D538-D545
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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CellCircuits: a database of protein network models
Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA 1 Division of Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
*To whom correspondence should be addressed. Tel: +1 858 822 4558; Fax: +1 858 822 4246; Email: trey{at}bioeng.ucsd.edu
Received August 16, 2006. Revised October 11, 2006. Accepted October 13, 2006.
CellCircuits (http://www.cellcircuits.org) is an open-access database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases of validated pathways. CellCircuits captures the output from an increasing number of approaches that screen molecular interaction networks to identify functional subnetworks, based on their correspondence with expression or phenotypic data, their internal structure or their conservation across species. This initial release catalogs 2019 computationally derived models drawn from 11 journal articles and spanning five organisms (yeast, worm, fly, Plasmodium falciparum and human). Models are available either as images or in machine-readable formats and can be queried by the names of proteins they contain or by their enriched biological functions. We envision CellCircuits as a clearinghouse in which theorists may distribute or revise models in need of validation and experimentalists may search for models or specific hypotheses relevant to their interests. We demonstrate how such a repository of network models is a novel systems biology resource by performing several meta-analyses not currently possible with existing databases.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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