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Supplemental Figure 1. Brain regions have distinct and overlapping sets of
differentially expressed genes at each time point. Overlap of differentially
expressed genes in cerebellum (yellow), hippocampus (green), hypothalamus
(red) and neocortex (blue) from each virgin pair-wise comparison: (A) virgin vs
PC14, (B) virgin vs PC16, (C) virgin vs PP1, (D) virgin vs PP3, and (E) virgin vs
PP10.
Similarities and differences in gene expression changes across the four
brain regions at each time point
To determine if each time point examined has a unique gene expression
response across the tissues examined, we determined the overlap of
differentially expressed genes in the four brain regions at each time point. For
the virgin and PC14 (Supplemental Figure 1A) and virgin to PC16
(Supplemental Figure 1B) comparisons, the hippocampus has the largest
number of genes with expression changes and the largest number of unique
genes with differential expression (green in Venn Diagram).
For these two
comparisons, the hippocampus and neocortex (green and blue in Venn Diagram)
have the largest number of overlapping genes, as well as the largest number of
genes with differential expression of the four brain regions (Figure 1D).
An
examination of the overlap of genes with differential expression in the virgin and
PP comparisons shows most brain regions do not have a large number of genes
that overlap, with the hippocampus and neocortex, again, generally showing the
greatest number (Supplemental Figure 1C-E).
Taken together, each brain
region has a unique molecular response at each time point examined, and the
hippocampus and neocortex have the most genes with expression differences in
common.
Supplementary Figure 2. Expression profile graphs for the genes that are
differentially expressed in all four brain region. The 49 genes’ expression
values (average FPKM across the replicates) were plotted. The Y-axis depicts
the range of the average FPKM values, and each colored line represents a
gene’s expression level.
Supplemental Figure 3. Line graphs of expression profiles for 49 genes that
are differentially expressed in all four brain regions. Each graph contains the
expression profile for each of the 49 genes, in each of the four brain regions. The
number at the left bottom corner of each profile graph is the cluster number from
the K-means cluster in (Figure 5). Beneath each diagram colored dots indicate:
1) Genes identified as differentially expressed in any pairwise comparison,
except the virgin pairwise comparisons (Violet; Figure 2B highlighted in grey). 2)
Genes that are induced with respect to virgins, in every brain region (Orange;
Figure 2C highlighted in grey). 3) Genes that are repressed with respect to
virgins, found in every brain region in every virgin pairwise comparison (Grey).
Supplemental Figure 4. Hierarchical cluster of genes that showed
significant and substantial changes in at least one of the pair-wise
comparison in the cerebellum. For each gene, averaged FPKM values were
used to generate the cluster. The hierarchical cluster was generated in GENE-E
using the ‘one minus pearson correlation’ metric, with the average linkage for the
linkage method. Gene Ontology terms, Disease and Pathway categories were
determined using the mousemine portal (http://www.mousemine.org) and are
indicated in the cluster.
Genes are marked with unique color to show the
specificity of their expression in the brain region, relative to the other brain
regions examined using the same criteria of significant and substantial changes
in expression. We assigned yellow (cerebellum), green (hippocampus), blue
(neocortex), and red (hypothalamus). Genes are marked with yellow if they are
only present in the cerebellum list. If one other region has differential expression
of that gene, it is marked with the color of "the second region". If a gene is
differentially expressed in more than 2 regions, it is marked purple.
Supplemental Figure 5: Hierarchical cluster of genes that showed
significant and substantial changes in at least one of the pair-wise
comparison in the hippocampus. For each gene, averaged FPKM values were
used to generate the cluster. The hierarchical cluster was generated in GENE-E
using the ‘one minus pearson correlation’ metric, with the average linkage for the
linkage method. Gene Ontology terms, Disease and Pathway categories were
determined using the mousemine portal (http://www.mousemine.org) and are
indicated in the cluster.
Genes are marked with unique color to show the
specificity of their expression in the brain region, relative to the other brain
regions examined using the same criteria of significant and substantial changes
in expression. We assigned yellow (cerebellum), green (hippocampus), blue
(neocortex), and red (hypothalamus). Genes are marked with green if they are
only present in the hippocampus list. If one other region has differential
expression of that gene, it is marked with the color of "the second region". If a
gene is differentially expressed in more than 2 regions, it is marked purple.
Supplemental Figure 6. Hierarchical cluster of genes that showed
significant and substantial changes in at least one of the pair-wise
comparison in the hypothalamus. For each gene, averaged FPKM values
were used to generate the cluster. The hierarchical cluster was generated in
GENE-E using the ‘one minus pearson correlation’ metric, with the average
linkage for the linkage method. Gene Ontology terms, Disease and Pathway
categories
were
determined
using
the
mousemine
portal
(http://www.mousemine.org) and are indicated in the cluster. Genes are marked
with unique color to show the specificity of their expression in the brain region,
relative to the other brain regions examined using the same criteria of significant
and substantial changes in expression. We assigned yellow (cerebellum), green
(hippocampus), blue (neocortex), and red (hypothalamus). Genes are marked
with red if they are only present in the hypothalamus list. If one other region has
differential expression of that gene, it is marked with the color of "the second
region". If a gene is differentially expressed in more than 2 regions, it is marked
purple.
Supplemental Figure 7. Hierarchical cluster of genes that showed
significant and substantial changes in at least one of the pair-wise
comparison in the hypothalamus. For each gene, averaged FPKM values
were used to generate the cluster. The hierarchical cluster was generated in
GENE-E using the ‘one minus pearson correlation’ metric, with the average
linkage for the linkage method. Gene Ontology terms, Disease and Pathway
categories
were
determined
using
the
mousemine
portal
(http://www.mousemine.org) and are indicated in the cluster. Genes are marked
with unique color to show the specificity of their expression in the brain region,
relative to the other brain regions examined using the same criteria of significant
and substantial changes in expression. We assigned yellow (cerebellum), green
(hippocampus), blue (neocortex), and red (hypothalamus). Genes are marked
with blue if they are only present in the neocortex list. If one other region has
differential expression of that gene, it is marked with the color of "the second
region". If a gene is differentially expressed in more than 2 regions, it is marked
purple.
Supplemental Figure 8. Hierarchical cluster of genes from a literature
survey, which previously have been shown to affect maternal behaviors
and/or have a role in pregnancy and reproductive functions. The cluster was
generated in GENE-E, using the ‘one minus pearson correlation’ metric for the
row distance measure and using average linkage as the linkage method. FPKM
values from the three replicates of each time point were averaged.
Supplementary Figure 9. Hierarchical cluster of genes with maintained
induced expression in the hypothalamus. The cluster was generated in
GENE-E, using the ‘one minus pearson correlation’ metric for the row distance
measure and using average linkage as the linkage method. FPKM values from
the three replicates of each time point were averaged.
Supplementary Figure 10. Hierarchical cluster of genes with maintained
induced expression in the hippocampus. The cluster was generated in GENEE, using the ‘one minus pearson correlation’ metric for the row distance measure
and using average linkage as the linkage method. FPKM values from the three
replicates of each time point were averaged.
Supplementary Figure 11. Hierarchical cluster of genes with maintained
induced expression in the neocortex. The cluster was generated in GENE-E,
using the ‘one minus pearson correlation’ metric for the row distance measure
and using average linkage as the linkage method. FPKM values from the three
replicates of each time point were averaged.
Supplementary Figure 12. Hierarchical cluster of genes with maintained
repressed expression in the hypothalamus. The cluster was generated in
GENE-E, using the ‘one minus pearson correlation’ metric for the row distance
measure and using average linkage as the linkage method. FPKM values from
the three replicates of each time point were averaged.
Supplementary Figure 13. Hierarchical cluster of genes with maintained
repressed expression in the hippocampus. The cluster was generated in
GENE-E, using the ‘one minus pearson correlation’ metric for the row distance
measure and using average linkage as the linkage method. FPKM values from
the three replicates of each time point were averaged.
Supplementary Figure 14. Hierarchical cluster of genes with maintained
repressed expression in the neocortex. The cluster was generated in GENEE, using the ‘one minus pearson correlation’ metric for the row distance measure
and using average linkage as the linkage method. FPKM values from the three
replicates of each time point were averaged.
Supplementary Figure 15. Principal component analysis plots showing
individual
library
samples.
hypothalamus, (D) neocortex.
(A)
cerebellum,
(B)
hippocampus,
(C)