Download Slide 1 - Genetics

30%
DE Genes
Array Probes
Cellular Localization
25%
20%
15%
10%
5%
25%
Molecular Function
other
cell wall
extracellular
ribosomes
plastids
mitochondria
cytoplasm
nucleus
plasma
membrane
intracellular
membranes
unknown
0%
DE Genes
Array Probes
20%
15%
10%
5%
20%
other
transporter
activity
DE Genes
Array Probes
Biological Process
15%
transcription
factor
other
binding
DNA or RNA
binding
protein
binding
structural
molecule
other
enzyme
kinase
activity
hydrolase
activity
transferase
activity
unknown
0%
10%
5%
DNA or RNA
metabolism
developmental
processes
energy
pathways
transport
signal
transduction
response to
stress
protein
metabolism
cell
organization
biological
cellular
physiological
metabolic
unknown
0%
Figure SOM1. Functional roles of the genes affected in zmet2-m1 mutants. Although the genes
localized on the intracellular membranes were slightly over-represented and the genes located in
plastids were slightly under-represented among the genes affected in the zmet2-m1 mutant plants,
these variations are likely insignificant.
Figure SOM2. The expression profile of maize genes in zmet2-m1 mutants based on the spotted long
oligonucleotide arrays. The expression of 179 genes defined as differentially expressed is shown for
three biological replicates for B73 and B73 zmet2-m1 plants.
4.0
2.0
1.0
0.5
0.25
B73
B73
zmet2-m1
Coloring
Figure SOM3. Correlation between Affymetrix and the long oligonucleotide array platforms. (A)
Correlation between log2 ratios between average signals from B73 and B73 zmet2-m1 samples
produced by two array platforms. (B) Scatter plots representing the correlation between
normalized values for both platforms. The values for genes determined as differentially expressed
in the Affymetrix data comparisons between B73 and B73 zmet2-m1genotype and present on the
long oligonucleotide array. The normalized average expressions for these genes from both
platforms were compared for B73 (circles) and the B73 zmet2-m1 plants (squares).
A
Long oligonucleotide array log2
(B73/B73 zmet2-m1)
4
3
2
1
0
-8
-6
-4
-2
-1
0
2
4
6
8
10
-2
-3
Affymetrix log2 (B73/B73 zmet2-m1)
-4
-5
-6
-7
Normalized Affymetrix log2
expression values
B
3.5
2.5
R = 0.85
R = 0.83
3
2
2.5
1.5
2
1.5
1
1
0.5
0.5
0
0
0
0.5
1
1.5
2
2.5
0
0.5
1
1.5
Normalized long oligonucleotide array log2 expression values
2
2.5
A
Gene expression
B
Group - 1down
B73
Mo17
B73 zmet2
Mo17 zmet2
2down
3down
4down
5down
1up
2up
3up
4up
5up
Figure SOM4. Classification of genes affected in zmet2-m1 mutant plants. (A) Clustering (Pearson
correlation) results for each of the five groups of genes. The profile shown is the average between
three biological replicates performed for each of four genotypes. Gene coloring is based on the
normalized expression values (normalized to value of 1) for two genetic backgrounds compared on
each part of the figure. (B) Examples of expression patterns observed for genes in the 10 different
classes. For this graph, the expression of one gene per group is shown as average normalized
expression values from three biological replicates. The specific expression values for all of the genes
in each of the groups are shown in Table SOM2.
4.0
2.0
1.0
0.5
0.25
Mo17
B73
Coloring
Figure SOM5. Genes affected in zmet2-m1 mutant plants exhibit large variation in expression
between wild type inbred lines B73 and Mo17. The expression of 126 genes defined as
differentially expressed in either of the comparisons is shown for three biological replicates for
B73 and Mo17. Gene coloring is based on the expression ratios between B73 and Mo17
genotypes. This comparison indicates that the genes most influenced by ZMET2 have large
baseline expression differences in wild-type lines, possibly due to methylation differences in
these lines.