Resolution:
## Figure 1.
PCA 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).
Mao |