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Fig. 5 | BMC Genomics

Fig. 5

From: Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development

Fig. 5

Hierarchical clustering suggested a stage-specific role for Nr2e1 in nervous system development. a Tag numbers for each of the 64 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; bold, key genes in this analysis. b Embryonic-stage-specific differences in expression profiles of “nervous system development” 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 a significant negative correlation was obtained with the tag ratios corresponding to the early neurogenic and early gliogenic stages (E13.5 vs. E17.5). No significance was obtained between the mid-neurogenic and early gliogenic stages (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

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