Figure 2.—

Self-organizing maps (SOM) depicting the patterns of genes whose expression showed a peak or a valley in only one sample relative to all others. The y-axis is the expression level of a sample as a fraction of the average expression in all 32 samples. Fractions less than zero were converted to negative reciprocals. The order of the data points on the x-axis from left to right is: E9, E9.5, E10, cochleae from E10.5 to E12, vestibular organs from E10.5 to E12, cochleae from E12.5 to E15, utricles from E12.5 to E15, saccules from E12.5 to E15, and NIE tissues from E9, E9.5–E10.5, and E11–E15. The centroid ID (beginning with c and ending with a colon) and the total number of genes with that particular centroid pattern are indicated above each square (centroid). The dark blue line traces the average expression of all genes within each centroid. The top and bottom red lines trace the expression pattern on the basis of maximal and minimal expression values for each data point, respectively. Note that the maximal and minimal values, from left to right, are not necessarily from the same probe set. (A) Genes downregulated in a NIE tissue sample relative to all IE tissue samples. (B) Genes downregulated in a NIE tissue sample as well as one IE tissue sample. (C) Genes upregulated in a NIE tissue sample relative to all IE tissue samples. (D) Genes upregulated in a NIE tissue sample as well as one IE tissue sample. (E) Genes upregulated in the cochlea at E15. These maps are shown in higher resolution in supplemental Figure 6.