MCA plots identify interesting biological subpopulations in mouse embryonic stem cells. A. MCA analysis reveals insight into the influence of Nanog on the Gbx2, Sox2 interaction. Gbx2 and Sox2 are significantly positively correlated when considering the entire Nanog+ compartment (quantiles 74% to 100% of Nanog, I). When considering the remaining Nanog- cells, the correlation is no longer significant (quantiles 0% to 74%, II). MCA plots reveal that the positive correlation in the Nanog+ compartment is due to just half of the compartment; the rest is uncorrelated (III). B. Gbx2 and Sox2 are uncorrelated when considering the whole Fgf5+ compartment (quantiles 82% to 100%, I). However, the top 10% are significantly positively correlated when considered alone (II). The Fgf5- compartment is significantly positively correlated (III), however, the majority of subpopulations in the Fgf5- compartment are not significantly correlated. See main text for a comparison of our findings with the previous report of Trott et al..