Figure 3.

Effects of chimerism on gene expression. (A) Venn diagram compares significant genes identified in the ANOVA model term chimerism × time and in the term chimerism. The pink circle represents chimerism × time (C × T), and the blue circle represents chimerism (C). (B) Gene expression volcano plots show both statistical significance and magnitude of gene expression change obtained from each experiment set and developmental time point. Each row represents a developmental stage and each column represents an experiment set. The x-axis represents the difference of M in chimera vs. in clone, where M = log₂(Cy3/Cy5 signal intensity), and y-axis represents the log₁₀(p) from the ANOVA model. The blue dots represent genes with statistically significant expression differences in clones vs. chimeras (p < 0.01) with a small differences in expression (fold-change < = 2), the red dots represent statistically significant genes (p < 0.01) with a large change in expression (fold-change > 2), and black dots represent statistically non-significant genes (p > =0.01). (C) Plots show numbers of significant genes identified at different developmental stages under different criteria. Left: number of genes that are statistically significant (p < 0.01). Right: number of genes that are statistically significant and with a large change in gene expression (p < 0.01 and fold-change > 2).