Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA304429 | ENA |
REPOSITORIES: ENA
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Project description:Sigurdsson2010 - Genome-scale metabolic model
of Mus Musculus (iMM1415)
This model is described in the article:
A detailed genome-wide
reconstruction of mouse metabolism based on human Recon 1.
Sigurdsson MI, Jamshidi N,
Steingrimsson E, Thiele I, Palsson BØ.
BMC Syst Biol 2010; 4: 140
Abstract:
BACKGROUND: Well-curated and validated network
reconstructions are extremely valuable tools in systems
biology. Detailed metabolic reconstructions of mammals have
recently emerged, including human reconstructions. They raise
the question if the various successful applications of
microbial reconstructions can be replicated in complex
organisms. RESULTS: We mapped the published, detailed
reconstruction of human metabolism (Recon 1) to other mammals.
By searching for genes homologous to Recon 1 genes within
mammalian genomes, we were able to create draft metabolic
reconstructions of five mammals, including the mouse. Each
draft reconstruction was created in compartmentalized and
non-compartmentalized version via two different approaches.
Using gap-filling algorithms, we were able to produce all
cellular components with three out of four versions of the
mouse metabolic reconstruction. We finalized a functional model
by iterative testing until it passed a predefined set of 260
validation tests. The reconstruction is the largest, most
comprehensive mouse reconstruction to-date, accounting for
1,415 genes coding for 2,212 gene-associated reactions and
1,514 non-gene-associated reactions.We tested the mouse model
for phenotype prediction capabilities. The majority of
predicted essential genes were also essential in vivo. However,
our non-tissue specific model was unable to predict gene
essentiality for many of the metabolic genes shown to be
essential in vivo. Our knockout simulation of the lipoprotein
lipase gene correlated well with experimental results,
suggesting that softer phenotypes can also be simulated.
CONCLUSIONS: We have created a high-quality mouse genome-scale
metabolic reconstruction, iMM1415 (Mus Musculus, 1415 genes).
We demonstrate that the mouse model can be used to perform
phenotype simulations, similar to models of microbe metabolism.
Since the mouse is an important experimental organism, this
model should become an essential tool for studying metabolic
phenotypes in mice, including outcomes from drug screening.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180055.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic 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.
2015-07-30 | MODEL1507180055 | BioModels
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Project description:PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea. Keywords: other
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