Dataset Information

Aho2010_RefRec_S_cerevisiae

ABSTRACT: This model is described in the article: Reconstruction and Validation of RefRec: A Global Model for the Yeast Molecular Interaction Network Aho T, Almusa H, Matilainen J, Larjo A, Ruusuvuori P, Aho K-L, Wilhelm T, Lähdesmäki H, Beyer A, Harju M, Chowdhury S, Leinonen K, Roos C and Yli-Harja O Plos One 5(5): e10662, 2010; doi: 10.1371/journal.pone.0010662 Abstract: Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is ~67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in ~590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our reconstruction is able to serve as a valuable resource in additional analyses involving objects from multiple molecular -omes. For that purpose, RefRec is freely available in the Systems Biology Markup Language format. This model originates from BioModels Database: A Database of Annotated Published Models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

SUBMITTER: Tommi Aho

PROVIDER: MODEL3883569319 | BioModels | 2005-01-01

REPOSITORIES: BioModels

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			Action	DRS
	MODEL3883569319?filename=MODEL3883569319-biopax2.owl	Owl
	MODEL3883569319?filename=MODEL3883569319-biopax3.owl	Owl
	MODEL3883569319?filename=MODEL3883569319.m	Other
	MODEL3883569319?filename=MODEL3883569319.pdf	Pdf
	MODEL3883569319?filename=MODEL3883569319.png	Other

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Publications

Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.

Aho Tommi T Almusa Henrikki H Matilainen Jukka J Larjo Antti A Ruusuvuori Pekka P Aho Kaisa-Leena KL Wilhelm Thomas T Lähdesmäki Harri H Beyer Andreas A Harju Manu M Chowdhury Sharif S Leinonen Kalle K Roos Christophe C Yli-Harja Olli O

PloS one 20100514 5

Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need ...[more]

PMID: 20498836

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