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MuTrack: a genome analysis system for large-scale mutagenesis in the mouse.

Baker EJ, Galloway L, Jackson B, Schmoyer D, Snoddy J - BMC Bioinformatics (2004)

Bottom Line: MuTrack demonstrates the effectiveness of using bioinformatics techniques in data collection, integration and analysis to identify unique result sets that are beyond the capacity of a solitary laboratory.By employing the research expertise of investigators at several institutions for a broad-ranging study, the TMGC has amplified the effectiveness of any one consortium member.The bioinformatics strategy presented here lends future collaborative efforts a template for a comprehensive approach to large-scale analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Baylor University, Waco, USA. Erich_Baker@Baylor.edu

ABSTRACT

Background: Modern biological research makes possible the comprehensive study and development of heritable mutations in the mouse model at high-throughput. Using techniques spanning genetics, molecular biology, histology, and behavioral science, researchers may examine, with varying degrees of granularity, numerous phenotypic aspects of mutant mouse strains directly pertinent to human disease states. Success of these and other genome-wide endeavors relies on a well-structured bioinformatics core that brings together investigators from widely dispersed institutions and enables them to seamlessly integrate data, observations and discussions.

Description: MuTrack was developed as the bioinformatics core for a large mouse phenotype screening effort. It is a comprehensive collection of on-line computational tools and tracks thousands of mutagenized mice from birth through senescence and death. It identifies the physical location of mice during an intensive phenotype screening process at several locations throughout the state of Tennessee and collects raw and processed experimental data from each domain. MuTrack's statistical package allows researchers to access a real-time analysis of mouse pedigrees for aberrant behavior, and subsequent recirculation and retesting. The end result is the classification of potential and actual heritable mutant mouse strains that become immediately available to outside researchers who have expressed interest in the mutant phenotype.

Conclusion: MuTrack demonstrates the effectiveness of using bioinformatics techniques in data collection, integration and analysis to identify unique result sets that are beyond the capacity of a solitary laboratory. By employing the research expertise of investigators at several institutions for a broad-ranging study, the TMGC has amplified the effectiveness of any one consortium member. The bioinformatics strategy presented here lends future collaborative efforts a template for a comprehensive approach to large-scale analysis.

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Sample chart of mouse weight by age. MuTrack users may access real-time data representations at various locations within the system. In this example, weights for mouse pedigree 268TNC have been examined and compared to mouse populations with similar mutagenic backgrounds. Unhealthy total weights or percentage of weight gains and loses are depicted by red bars. Systems such as these allow MuTrack users the ability to easily assess various aspects of mouse health, location, or testing status.
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Figure 5: Sample chart of mouse weight by age. MuTrack users may access real-time data representations at various locations within the system. In this example, weights for mouse pedigree 268TNC have been examined and compared to mouse populations with similar mutagenic backgrounds. Unhealthy total weights or percentage of weight gains and loses are depicted by red bars. Systems such as these allow MuTrack users the ability to easily assess various aspects of mouse health, location, or testing status.

Mentions: In order to ensure that publicly defined mutations are not released before a consensus of their proven heritability has been reached, the computational tools are separated into two different web domains. Public users may enter the "open" statistical pages for MuTrack. These pages allow public users to search mice located in any domain for deviants based on standard deviations from the mean. These tests are often used by TMGC researchers as a rudimentary analysis of their submitted data and do not represent precise statistical outliers. Figure 4 is a graphical representation of how members of mouse pedigree 047TNJ faired in one particular test in the Ethanol domain. Other relative individuals from different pedigrees are placed along the horizontal access for comparison. Public MuTrack access also allows users to view graphical representations of data from areas outside of the statistic pages. Figure 5 demonstrates the weight progress of mice belonging to pedigree 268TNC, available in the main Aging Weights domain. The red bar may indicate a weight gain that is significantly greater or less than that of comparable mice. This allows researchers to quickly gauge the health of the testing pedigree stock.


MuTrack: a genome analysis system for large-scale mutagenesis in the mouse.

Baker EJ, Galloway L, Jackson B, Schmoyer D, Snoddy J - BMC Bioinformatics (2004)

Sample chart of mouse weight by age. MuTrack users may access real-time data representations at various locations within the system. In this example, weights for mouse pedigree 268TNC have been examined and compared to mouse populations with similar mutagenic backgrounds. Unhealthy total weights or percentage of weight gains and loses are depicted by red bars. Systems such as these allow MuTrack users the ability to easily assess various aspects of mouse health, location, or testing status.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC370570&req=5

Figure 5: Sample chart of mouse weight by age. MuTrack users may access real-time data representations at various locations within the system. In this example, weights for mouse pedigree 268TNC have been examined and compared to mouse populations with similar mutagenic backgrounds. Unhealthy total weights or percentage of weight gains and loses are depicted by red bars. Systems such as these allow MuTrack users the ability to easily assess various aspects of mouse health, location, or testing status.
Mentions: In order to ensure that publicly defined mutations are not released before a consensus of their proven heritability has been reached, the computational tools are separated into two different web domains. Public users may enter the "open" statistical pages for MuTrack. These pages allow public users to search mice located in any domain for deviants based on standard deviations from the mean. These tests are often used by TMGC researchers as a rudimentary analysis of their submitted data and do not represent precise statistical outliers. Figure 4 is a graphical representation of how members of mouse pedigree 047TNJ faired in one particular test in the Ethanol domain. Other relative individuals from different pedigrees are placed along the horizontal access for comparison. Public MuTrack access also allows users to view graphical representations of data from areas outside of the statistic pages. Figure 5 demonstrates the weight progress of mice belonging to pedigree 268TNC, available in the main Aging Weights domain. The red bar may indicate a weight gain that is significantly greater or less than that of comparable mice. This allows researchers to quickly gauge the health of the testing pedigree stock.

Bottom Line: MuTrack demonstrates the effectiveness of using bioinformatics techniques in data collection, integration and analysis to identify unique result sets that are beyond the capacity of a solitary laboratory.By employing the research expertise of investigators at several institutions for a broad-ranging study, the TMGC has amplified the effectiveness of any one consortium member.The bioinformatics strategy presented here lends future collaborative efforts a template for a comprehensive approach to large-scale analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Baylor University, Waco, USA. Erich_Baker@Baylor.edu

ABSTRACT

Background: Modern biological research makes possible the comprehensive study and development of heritable mutations in the mouse model at high-throughput. Using techniques spanning genetics, molecular biology, histology, and behavioral science, researchers may examine, with varying degrees of granularity, numerous phenotypic aspects of mutant mouse strains directly pertinent to human disease states. Success of these and other genome-wide endeavors relies on a well-structured bioinformatics core that brings together investigators from widely dispersed institutions and enables them to seamlessly integrate data, observations and discussions.

Description: MuTrack was developed as the bioinformatics core for a large mouse phenotype screening effort. It is a comprehensive collection of on-line computational tools and tracks thousands of mutagenized mice from birth through senescence and death. It identifies the physical location of mice during an intensive phenotype screening process at several locations throughout the state of Tennessee and collects raw and processed experimental data from each domain. MuTrack's statistical package allows researchers to access a real-time analysis of mouse pedigrees for aberrant behavior, and subsequent recirculation and retesting. The end result is the classification of potential and actual heritable mutant mouse strains that become immediately available to outside researchers who have expressed interest in the mutant phenotype.

Conclusion: MuTrack demonstrates the effectiveness of using bioinformatics techniques in data collection, integration and analysis to identify unique result sets that are beyond the capacity of a solitary laboratory. By employing the research expertise of investigators at several institutions for a broad-ranging study, the TMGC has amplified the effectiveness of any one consortium member. The bioinformatics strategy presented here lends future collaborative efforts a template for a comprehensive approach to large-scale analysis.

Show MeSH