Figure 1From: Primary and secondary transcriptional effects in the developing human Down syndrome brain and heartPCA was used to visually assess the major sources of variation in the expression data. For each of the four panels, each data point represents a sample; there are 25 samples total. (a) PCA applied to chromosome 21 genes. The x-axis represents the first PC (accounting for 41% of the variance) and the y-axis represents the second PC (accounting for 21.2%). The graph is based on expression values for all 253 probe sets assigned to chromosome 21. This showed that the largest source of variability was due to tissue/cell type, accounting for 62.2% of the variance in the data. (b) PCA applied to chromosome 21 genes. The x-axis corresponds to the third PC, and the y-axis corresponds to the second PC. The third PC showed a separation of trisomic from euploid samples based on gene expression, accounting for 17.2% of the variance in the data. (c) PCA applied to non-chromosome 21 genes. The first two PCs (x- and y-axis) using expression values for genes assigned to all other chromosomes also showed that the largest source of variance was due to tissue (77.4% of total variance). These observations are similar to the results in panel a. (d) PCA applied to non-chromosome 21 genes. The x- and y-axis correspond to the third and second PCs, respectively. In contrast to the results of panel b, the third PC failed to show separation of trisomic from euploid samples (6.9% of total variance). The ellipsoids represent three standard deviations beyond the centroid of each tissue group. Data points correspond to samples (red, Down syndrome; blue, euploid) within a group (cerebrum, diamond symbols on data points, and green ellipsoid; cerebellum, square symbols on data points and blue ellipsoid; astrocyte, triangle symbols on data points and red ellipsoid; heart, hexagon symbols on data points and orange ellipsoid).Back to article page