CellCircuits: a database of protein network models.
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.
Mak
H Craig
HC
Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA.
Daly
Mike
M
Gruebel
Bianca
B
Ideker
Trey
T
D000818:Animals; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism; D030562:Databases, Protein; D029721:Drosophila Proteins / Q000378:metabolism; D006801:Humans; D020407:Internet; D015201:Meta-Analysis as Topic; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010963:Plasmodium falciparum / Q000378:metabolism; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology; D014584:User-Computer Interface
D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins