CellCircuits: a database of protein network models

Abstract

CellCircuits () 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.

Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context

“…This expression data was combined with a yeast cell cycle protein interaction graph constructed by de Lichtenberg et al [12] and available from the Cell Circuits database [29]. Cellular location information was obtained from the Yeast Protein Localization Server [13].…”

Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology

“…Most representations of these networks show a set of nodes (the genes/proteins) connected by edges whenever there is some form of interaction between them (e.g. [315]). This kind of representation is ambiguous and prevents direct utilization of the networks for the generation of mathematical models.…”

Protein-Protein Interactions and Disease

“…• Cell Circuits (Mak et al, 2007) for comparison of hand-curated pathway models to hypothetical models derived from large-scale 'omic' data.…”