Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract MouseCyc is a database of curated biochemical pathways data for the laboratory mouse that can be integrated with functional and phenotypic data from the Mouse Genome Informatics (MGI) database.

The availability of the complete ‘genome sequence’ for the laboratory mouse provides an advanced platform for predicting genes and other genome features.

However, building a catalog of genome annotations is just the beginning for biology in a “post-genome” era.

To derive new insights into fundamental biological processes using complete genome sequences will require understanding how genome features interact in pathways and networks in the cell and how perturbations of these interactions contribute to disease processes.

Toward this end, the manufacturers have implemented a new database of curated ‘biochemical pathways’ for the laboratory mouse called MouseCyc.

The MouseCyc database represents a significant advance for biomedical researchers wanting to access mouse genetic and genomic data in the context of physiological and cellular processes.

The initial focus for the development of MouseCyc is on metabolism and includes such ‘cell level processes’ as biosynthesis, degradation, energy production, and detoxification.

MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of ‘biological knowledge’ for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database.

MouseCyc facilitates the use of the laboratory mouse as a model system for understanding human biology and disease processes in three (3) ways.

First, the database provides a means by which the available wealth of biological knowledge about mouse genes can be organized in the context of biochemical pathways.

Second, the query and analysis tools for the database serve as a means for researchers to ‘view and analyze’ genome scale experiments by overlaying these data onto global views of the curated mouse metabolome.

Finally, MouseCyc supports direct comparisons of metabolic processes and pathways between mouse and human; comparisons that may be critical to understanding both the power and the biological limitations of using mouse models of human disease.

MouseCyc Implementation --

Initial PathoLogic analysis, manual curation, and PathoLogic incremental updates -

The initial implementation of the MouseCyc pathway genome database using the PathoLogic prediction software (see G6G Abstract Number 20235), with Pathway Tools resulted in the prediction of 304 pathways, 1,832 enzymatic reactions, and 5 transport reactions.

Following the automated build of MouseCyc, the predicted reactions and pathways were evaluated and refined manually.

The initial manual curation effort focused on identifying pathways and reactions, predicted by PathoLogic, that were Not relevant to mammalian biochemistry (e.g., biosynthesis of essential amino acids).

The manual curation process resulted in the elimination of 135 non- mammalian pathways (45% of the pathways predicted for mouse by PathoLogic) from the database.

The high percentage of predicted pathways in MouseCyc that required manual reassignment was Not surprising given that, for historic reasons, the MetaCyc reference database (see G6G Abstract Number 20232), used by PathoLogic is somewhat biased toward prokaryotic and plant biochemistry.

Finally, PathoLogic’s Transport Inference Parser (TIP) utility was used to identify putative transport reactions.

For the mouse genome, TIP predicted 80 transport reactions and 542 transporters.

MouseCyc Data Access features/capabilities include:

1) Search the MouseCyc database.

2) Browse the pathway ontology in the MouseCyc database.

3) Browse all pathways represented in MouseCyc.

4) Browse a list of all genes in MouseCyc.

5) Browse a list of all proteins in MouseCyc according to their activity.

6) Browse a list of all compounds represented in MouseCyc.

7) Overlay experimental data onto the Pathway Tools Omics Viewer (see G6G Abstract Number 20237).

8) Display an Example of Omics Viewer files.

9) Generate a mouse ‘metabolic map’.

System Requirements



Manufacturer Web Site MouseCyc

Price Contact manufacturer.

G6G Abstract Number 20462

G6G Manufacturer Number 104089