NAR Molecular Biology Database Collection entry number 980
Mak H.C.1, Daly M.2, Gruebel B.2 and Ideker T.2
1Division of Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
2Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

Database Description

CellCircuits (http://www.cellcircuits.org) is an open-access database of molecular network models, designed to bridge the gap between databases of individual pair-wise 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 eleven 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.


We acknowledge funding from the National Science Foundation (NSF 0425926) and thank the members of the Ideker lab for testing and suggesting improvements to the web interface.

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