Biology Reference
In-Depth Information
a)
b)
YBL091C-A
YNL162W
160
40
1
1
140
35
120
30
100
25
6
6
80
20
60
15
40
10
20
5
0
0
0
5
10
15
20
0
50
100
150
200
250
TL
TL
c)
d)
YHR029C
YLR084C
24
1.6
1
6
21
1.4
18
1.2
15
1
12
0.8
1
9
0.6
6
0.4
6
3
0.2
0
0
0
20
40
60
80
0
10
20
30
40
TL
TL
Fig. 12.1. Plots of the fold changes in transcription rates (
TR
) against those of transcript levels (
TL
)
measured in budding yeast at 6 time points (1 = 0 min, 2 = 5 min, 3 = 120 min, 4 = 360 min, 5 = 450
min, and 6 = 850 min) after the glucose-galactose shift.
12.2.3.
Measuring mRNA or Transcript Levels (
TL
)
The total RNA isolated from the same cell culture used in the previous section was
reverse-transcribed into cDNA in the presence of [
α
33
P]dCTP [10]. The labeled
cDNAs were purified and hybridized under the same conditions as described for
GRO
in order to minimize the variability due to artifacts of DNA membrane ar-
rays. Again, the raw
TL
data in arbitrary units measured in triplicates at 6 time
points are available at
http://evalga.uv.es/scsie-docs/chipsdna/chipsdna-e.html
.
−
12.2.4.
The
TL-TR
Plots
The
TL
and
TR
data measured as described in the previous sections can be visu-
alized in a 2-dimensional plane as shown in Fig. 12.1. The genes depicted in this
figure were randomly chosen out of the 5,725 genes showing no missing values in
their triplicate measurements of
TL
and
TR
. The notation given on the top of each
figure is the name of the open reading frame (ORF) whose
TL
and TR values were
measured. The trajectory of each plot can be divided into 5 segments or vectors
bounded by two time points (
e.g.
, vector 1-2 between 0 to 5 min after the glucose-
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