NN
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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
108779714
Start End
108779924 132723271 135944511 135944738
Distance (Mb) from beginning of chromosome
132748377GeneGene Gene Gene
Genes and Chromosomes Genes and Chromosomes in the GISin the GIS
The QuestionsThe Questions
How do genes respond differently in How do genes respond differently in parous and nulliparous mice?parous and nulliparous mice?
Can GIS and spatial analysis be used Can GIS and spatial analysis be used in genetic research?in genetic research?
Is there a spatial organization of Is there a spatial organization of gene expression based on biological gene expression based on biological experience ?experience ?
21, 000 genes on 21 chromosomes21, 000 genes on 21 chromosomes Starting and Ending LocationsStarting and Ending Locations Used Cartesian Coordinate SystemUsed Cartesian Coordinate System
X = starting location X = starting location Y = chromosome # (for display)Y = chromosome # (for display)
Mapped as points for analysisMapped as points for analysis
Mapping the Mouse Genome
chromosome
Mapping the Mapping the Mouse GenomeMouse Genome
chromosome
Differential Gene Expression Differential Gene Expression in the Mouse Genomein the Mouse Genome
Mb Units
The Spatial Scan StatisticThe Spatial Scan Statistic
Spatial Autocorrelation
chromosome
Clustering of Clustering of Gene ExpressionGene Expression
Mapping the gene in a GIS is now Mapping the gene in a GIS is now possiblepossible
Clustering of up-or down-regulated Clustering of up-or down-regulated genes in response to paritygenes in response to parity
Genes exhibit coordinated expression Genes exhibit coordinated expression based on their spatial locationbased on their spatial location
Mechanism for protective effect of Mechanism for protective effect of parityparity
ConclusionsConclusions
Next StepsNext Steps
What are the functions of the What are the functions of the individual genes in clusters?individual genes in clusters?
Are they related to disruption of Are they related to disruption of oncogenesis?oncogenesis?
Examine the differential response of Examine the differential response of parity to radiationparity to radiation
CollaborationCollaboration
Thank youThank you
Jane Garb*
Joseph Jerry+§
Mary Hagen§
Jennifer Friderici*
Sallie Schneider§+
Karen Dunphy§
Amy Roberts§
* Baystate Health
+ Pioneer Valley Life Sciences Institute
§ University of Massachusetts
Problems with Spatial analysis of Gene Problems with Spatial analysis of Gene Expression levelsExpression levels
relative gene location on the relative gene location on the chromosome at equally spaced chromosome at equally spaced intervalsintervals
Pre-defined region of the Pre-defined region of the chromosomechromosome
False DiscoveryFalse Discovery
Resolves Statistical Issues with Resolves Statistical Issues with Previous StudiesPrevious Studies
Analyzes actual distanceAnalyzes actual distance
Not Limited to one scaleNot Limited to one scale
Controls for multiple testsControls for multiple tests
Gene locations analyzed at actual Gene locations analyzed at actual location rather than at regularly location rather than at regularly space intervals space intervals