Biology Reference
In-Depth Information
1. (
ΔG
AB
) = Horizontal Group
Δ
XY
=
(
Δ
G
2
+
Δ
P
2
)
1/2
2. (
Δ
P
AB
) = Vertical Group
3. (
ΔG
AB
, ΔP
AB
) = Diagonal Group
Fig. 12.19 The three possible mechanisms giving rise to the difference between two points, X and
Y in the GSvPD plot. Mechanism 1
¼
the distance,
D
XY
¼
((G
2
G
1
)
2
+(P
2
P
1
)
2
)
1/2
,is
determined by the
genotypic
difference only between RNA pair, A and B. Mechanism 2
¼
the
distance is determined by the
phenotypic
difference only between the RNA pair. Mechanism
3
¼
The distance is determined by both the
genotypic
and the
phenotypic
differences between the
RNA pair
B, and
D
P
AB
is the phenotypic difference between the same RNA pair. So when we
compute the distance,
D
XY, between two points, X (G
1
,P
1
) and Y (G
2
,P
2
), in the
GSvPD plot using the Pythagorean formula, there are three distinct mechanisms by
which the difference can arise as explained in Fig.
12.19
.
However, in order to simplify the argument, it will be assumed in this topic
(e.g., Fig.
12.17
) that the mechanism underlying the metric (i.e., distance measure-
ment) in the GSvPD plot is due to Mechanism 3 only. If the three mechanisms defined
in Fig.
12.19
all have an equal probability of being realized, any conclusion made on
the basis of the simplifying assumption would have approximately 33% of being
correct. When more information about the mechanism of interactions among
RNA pairs is available and taken into account, this probability could be increased
toward unity.
12.10 Rule-Governed Creativity (RGC)
in Transcriptomics: Microarray Evidence
The points in the GSvPD plots, e.g., Figs.
12.17
and
12.18
, can be divided into four
groups as explained in Fig.
12.20
. More than 95% of the RNA pairs belong to the
self-regulatory group, and only less than 5% belong to the “other-regulatory” group.
In other words, during the glucose-galactose shift, most of the structural genes of
the budding yeast cells contribute to regulating their own transcript levels, and this
self-regulatory fraction
of structural genes may vary depending on the environmen-
tal conditions under which RNA levels are measured.
Group
A
comprises the RNA pairs whose coordinates lie above the diagonal line,
and thus their intracellular concentrations are controlled by factors other than their
structural genes. These RNA pairs belong to the group of what will be referred to as
the “other-regulatory” or “other-regulated” genes, meaning that these genes are
regulated by other genes or regulatory DNA regions including promoters,
enhancers, and silencers (see Fig.
12.17
). Group
B
represents the RNA pairs
whose coordinates lie below the diagonal line. The intracellular concentrations of
