|
|
|
|
|
|
|
||||
| Home Help Feedback Subscriptions Archive Search Table of Contents | ||||
|
Fig. 2. Comprehensive identification of genes demonstrating differences in
expression along the rostrocaudal axis of the developing neocortex. (A)
Rostrocaudal gene expression differences in the neocortex at E11.5. Scatter
plot of observed gene expression ratios against expected ratios, as calculated
using the significance analysis of microarrays algorithm (SAM, see text for
details). (B) Clustering of genes from A with rostrocaudal expression
differences at E11.5 passing a 5% false discovery rate cutoff in SAM. Each
column represents a single microarray and each row expression data for a
single gene. Alternate microarrays are dye-swaps (technical replicate) of the
preceeding microarray, the ratios of which have been reversed. The 10
microarrays shown here represent five dye-swapped pairs, and the analysis of
five separate samples of rostral and caudal neocortical tissue. The numbers of
rostral and caudal genes identified are indicated in brackets. By convention,
positive differences in expression (upregulation) are represented in red, and
negative differences (downregulation) in green, with the colour intensity
reflecting the magnitude of the underlying expression ratio. (C) Rostrocaudal
gene expression differences at E13.5. Scatter plot of observed gene expression
ratios against expected ratios, as calculated using the significance analysis
of microarrays algorithm (SAM, see text for details). (D) Clustering of genes
from C with rostrocaudal expression differences at E13.5 passing a 5% false
discovery rate cutoff in SAM. (E) Combined analysis of E11.5 and E13.5 data.
Scatter plot of observed gene expression ratios against expected ratios, as
calculated using the significance analysis of microarrays algorithm (SAM, see
text for details). (F) Clustering of genes passing 5% false discovery rate
cutoff in SAM from E. (G) An array screen for genes demonstrating periodic
gene expression along the rostrocaudal axis of the developing neocortex. E13
neocortices were divided into thirds along the rostrocaudal axis, and tissue
pooled from single cortical hemispheres from four different embryos to
generate three separate pools of tissue for each third (three pools each of
rostral, middle and caudal tissue). Global gene expression was compared
between every possible pair of types of pool in a set of 18 independent array
hybridisations. The resulting cluster of genes identified as reproducibly
rostrally or caudally enriched, compared with middle and rostral or caudal
tissue, is shown. (H) Genes identified as more highly expressed in the caudal
neocortex and expressed in gradients, or as more highly expressed in the
rostral neocortex and expressed in gradients, show the appropriate rank order
of expression by microarray analysis. For example, the magnitude of the
expression ratio is highest comparing caudal and rostral samples, and these
genes are expressed at higher levels in caudal samples than middle, and in
middle samples than rostral.
|
