Fig. 7: Selection of gene space in MERFISH measured ≈ 500 genes and illustration of within region and between region variance.
a–l Show relative expression of genes with high and low mutual information (MI) scores across two MERFISH tissue sections at coronal levels a–f Z = 385 and g–l Z = 485 in CCFv3 coordinates, respectively. Genes with highest mutual information scores a–c, g–i are Gfap, Trp53i11, Wipf3) and lowest d–f, j–l are Chodl, Brs3, Hpse2. m–x Exhibit empirical distribution of genes in slices 1 and 2 deformed to corresponding CCFv3 slice. m, p, s, v Show probability of single m, s low MI gene or p, v high MI gene per atlas particle at 50-μm resolution. n, q, t, w Show average probability of single n, t low MI gene or q, w high MI gene. o, r, u, x Show variance within each region of probability of single o, u low MI gene or r, x high MI gene. y indicates the number of pairs of regions with significant differences in probabilities for three genes with high MI and low MI, with significance calculated at 0.05 but corrected for multiple comparisons with bonferroni correction as 0.00003 and 0.00001 based on the number of regions as 60 and 94 in slice 1 and 2 respectively. All computed p-values provided in Supplementary Data 3.
