Fig. 3

Hierarchical clustering suggested a stage-specific role for Nr2e1 in neocortex development. a Tag numbers for each of the corresponding 1279 genes were retrieved from DiscoverySpace and hierarchical-clustering was performed prior to visualization in a heat-map; displaying significant-differential-tag ratios from Wt vs. Nr2e1 ^frc/frc libraries. The relative expression was calculated based on the tag ratios from Wt vs. Nr2e1 ^frc/frc libraries and corrected to account for library sizes; (observed tag counts/total useful tags) X 100,000. Tags having a count value of “0” (no expressed tags) were adjusted to a value of “1” for fold change calculations only. Green, down; red, up; black, no difference; grey, no expressed tags. b Embryonic-stage-specific differences in expression profiles of the 1279 differently abundant genes in neocortex development of Wt vs. Nr2e1 ^frc/frc embryos was demonstrated using Spearman rank correlation. Spearman rank correlation was performed on gene lists from pairs of embryonic stages using STATISTICA. Results revealed a significant positive correlation between the lists corresponding to early and mid-neurogenic stages (E13.5 vs. E15.5); whereas significant negative correlations were obtained with the tag ratios corresponding to the early and mid-neurogenic stages versus the early gliogenic stages (E13.5 vs. E17.5, and E15.5 vs. E17.5). Column one presents the time-point comparisons; column two, the valid number of genes included in the analysis; columns three and four, the corresponding R and P values obtained by Spearman rank correlation