Quek2008 - Genome-scale metabolic network of Mus musculus

Quek2008 - Genome-scale metabolic network of
Mus musculus

This model is described in the article:

On the reconstruction of the
Mus musculus genome-scale metabolic network model.

Quek LE, Nielsen LK.
Genome Inform 2008; 21: 89-100
Abstract:

Genome-scale metabolic modeling is a systems-based approach
that attempts to capture the metabolic complexity of the whole
cell, for the purpose of gaining insight into metabolic
function and regulation. This is achieved by organizing the
metabolic components and their corresponding interactions into
a single context. The reconstruction process is a challenging
and laborious task, especially during the stage of manual
curation. For the mouse genome-scale metabolic model, however,
we were able to rapidly reconstruct a compartmentalized model
from well-curated metabolic databases online. The prototype
model was comprehensive. Apart from minor compound naming and
compartmentalization issues, only nine additional reactions
without gene associations were added during model curation
before the model was able to simulate growth in silico. Further
curation led to a metabolic model that consists of 1399 genes
mapped to 1757 reactions, with a total of 2037 reactions
compartmentalized into the cytoplasm and mitochondria, capable
of reproducing metabolic functions inferred from literatures.
The reconstruction is made more tractable by developing a
formal system to update the model against online databases.
Effectively, we can focus our curation efforts into
establishing better model annotations and gene-protein-reaction
associations within the core metabolism, while relying on
genome and proteome databases to build new annotations for
peripheral pathways, which may bear less relevance to our
modeling interest.

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MODEL1507180067.
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