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Table 1.

Factor analysis of subnuclear organization

Factor Common domain characteristic Constituent parameters Loadings
A   Size properties   Mean domain size   0.66  
   Standard deviation in domain size   0.94  
   Variance in domain size   0.93  
   Skewness in domain size   0.90  
   Kurtosis in domain size   0.90  
   Coefficient of variation in domain size   0.95  
   Index of dispersion in domain size   0.97  
B   Packing   Mean domain nearest neighbor distance (observed), Ro   0.94  
   Median domain nearest neighbor distance   0.91  
   Domain density   −0.91  
   Mean domain nearest neighbor distance (expected), Re   0.90  
   Variance in domain nearest neighbor distance (expected), Ve   0.88  
C   Spatial randomness   Variance in domain nearest neighbor distance (observed), Vo   0.87  
   Standard deviation in domain nearest neighbor distance   0.85  
   Coefficient of variation in domain nearest neighbor distance   0.95  
   Index of dispersion in domain nearest neighbor distance   0.92  
   Vo/Ve   0.96  
Factor Common domain characteristic Constituent parameters Loadings
A   Size properties   Mean domain size   0.66  
   Standard deviation in domain size   0.94  
   Variance in domain size   0.93  
   Skewness in domain size   0.90  
   Kurtosis in domain size   0.90  
   Coefficient of variation in domain size   0.95  
   Index of dispersion in domain size   0.97  
B   Packing   Mean domain nearest neighbor distance (observed), Ro   0.94  
   Median domain nearest neighbor distance   0.91  
   Domain density   −0.91  
   Mean domain nearest neighbor distance (expected), Re   0.90  
   Variance in domain nearest neighbor distance (expected), Ve   0.88  
C   Spatial randomness   Variance in domain nearest neighbor distance (observed), Vo   0.87  
   Standard deviation in domain nearest neighbor distance   0.85  
   Coefficient of variation in domain nearest neighbor distance   0.95  
   Index of dispersion in domain nearest neighbor distance   0.92  
   Vo/Ve   0.96  

The covariance structure between the 25 subnuclear organization parameters measured on wild-type and mutant images (n=330) indicates that there is a large degree of correlation between parameters (data not shown). Factor analysis was carried out to represent the observed subnuclear organization parameters in terms of a smaller number of uncorrelated variables. The strategy reduces the 25 parameters to a subset of three factors that retain the information (variability) contained within the entire data set. In multivariate analysis, `factors' reflect groups of correlated parameters that are related to a common property of subnuclear organization. Each of the factors has a biological interpretation based upon the grouped subnuclear organization parameters. We restricted our analysis to the first three factors (referred to as A, B and C), as they reflect meaningful aspects of the domain spatial. Factor A, which represents `domain size properties', accounts for approximately 30% of the information describing the subnuclear organization of the wild-type Runx and mutant images (i.e. 30% of the variation). The domain size properties are highly correlated with parameters that describe the variability in domain size and to a lesser degree the mean domain size. Factor B, which reflects `domain packing', describes 23% of the variation and is directly correlated with parameters that characterize the mean nearest neighbor distances and inversely related to domain density. `Packing' indicates that this factor relates the number of domains to the distances between domains. Factor C, which reflects `domain spatial randomness', describes 10% of the variation and is directly correlated with parameters that described the variability in domain nearest neighbor distance.

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