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.