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Mapping the Genome: A Spatial Analysis of Gene Expression on the Mouse Chromosome

Mapping the Genome: A Spatial Analysis of Gene Expression on the Mouse Chromosome. Jane Garb * Joseph Jerry +§ Mary Hagen § Jennifer Friderici * Sallie Schneider §+ Karen Dunphy § Amy Roberts § * Baystate Health + Pioneer Valley Life Sciences Institute § University of Massachusetts.

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Mapping the Genome: A Spatial Analysis of Gene Expression on the Mouse Chromosome

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  1. Mapping the Genome: A Spatial Analysis of Gene Expression on the Mouse Chromosome Jane Garb* Joseph Jerry+§ Mary Hagen§ Jennifer Friderici* Sallie Schneider§+ Karen Dunphy§ Amy Roberts§ * Baystate Health + Pioneer Valley Life Sciences Institute § University of Massachusetts

  2. Distance (Mb) from beginning of chromosome 108779714 108779924 132723271 132748377 135944511 135944738 Gene Gene Gene Gene Start End Genes and Chromosomes in the GIS

  3. The Questions • How do genes respond differently in parous and nulliparous mice? • Can GIS and spatial analysis be used in genetic research? • Is there a spatial organization of gene expression based on biological experience ?

  4. Mapping the Mouse Genome • 21, 000 genes on 21 chromosomes • Starting and Ending Locations • Used Cartesian Coordinate System • X = starting location • Y = chromosome # (for display) • Mapped as points for analysis

  5. Mapping the Mouse Genome chromosome

  6. Mb Units chromosome Differential Gene Expression in the Mouse Genome

  7. The Spatial Scan Statistic Spatial Autocorrelation

  8. chromosome Clustering of Gene Expression

  9. Conclusions • Mapping the gene in a GIS is now possible • Clustering of up-or down-regulated genes in response to parity • Genes exhibit coordinated expression based on their spatial location • Mechanism for protective effect of parity

  10. Next Steps • What are the functions of the individual genes in clusters? • Are they related to disruption of oncogenesis? • Examine the differential response of parity to radiation

  11. Collaboration

  12. Jane Garb* Joseph Jerry+§ Mary Hagen§ Jennifer Friderici* Sallie Schneider§+ Karen Dunphy§ Amy Roberts§ * Baystate Health + Pioneer Valley Life Sciences Institute § University of Massachusetts Thank you

  13. Problems with Spatial analysis of Gene Expression levels • relative gene location on the chromosome at equally spaced intervals • Pre-defined region of the chromosome • False Discovery

  14. Resolves Statistical Issues with Previous Studies • Analyzes actual distance • Not Limited to one scale • Controls for multiple tests • Gene locations analyzed at actual location rather than at regularly space intervals

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