Biology Reference
In-Depth Information
D
TR
3
4
2
DTL
5
1
9
6
8
7
Fig. 12.8 The “unit circle” whose
x
-axis indicates the changes in TL values (
D
TL) and the
y
-axis
indicates the changes in TR values (
D
TR) of a trajectory in the TL-TR plot (see Fig.
12.6
).
The direction of the radial arrow coincides with the direction of the component vector (or segment)
of the trajectories in the TL-TR plot. The angle of the radial arrow is divided into eight ranges
defined as follows: 1
177 ~ 183;
6
¼
184 ~ 266; 7
¼
267 ~ 273; 8
¼
274 ~ 356. Range 9 indicates the situation where neither
TL nor TR underwent any measurable changes (Reproduced from Ji et al. 2009a)
¼
357 ~ 3; 2
¼
4 ~ 86; 3
¼
87 ~ 93; 4
¼
94 ~ 176; 5
¼
is associated with mechanism in which TL increases despite the fact that TR
decreases, etc. Thus, it is logical to equate these groups with their underlying
mechanisms (or modules) of RNA metabolism. We may refer to such modules as
“mechanistic modules of RNA metabolism,” “mechanisms of RNA metabolism,”
or “modules of RNA metabolism.” These terms are related to “ribonomics” defined
by Keene (2006) as the genome-wide study of RNA metabolism in cells.
The five angles characterizing the trajectory of each of the 5,725 genes were
calculated from their TL and TR values as follows. The angle
Y
determining the
direction of the segment from the ith time point to the (i + 1)th time point in a TL
vs. TR plot with coordinates (x
i
,y
i
) and (x
i+1
,y
i+1
), respectively, was calculated
from the relation
Y ¼
tan
1
0
if both
[(y
i+1
y
i
)/(x
i+1
x
i
)] +
a
, where
a ¼
180
if either the numerator is
positive and the denominator is negative or both the numerator and the denominator
are negative, and
a ¼
the numerator and the denominator are positive,
a ¼
360
if the numerator is negative but the denominator is
positive. From the set of 5,184 pairs of TR and TL data measured at six time points,
we calculated a total of 5
25,920 angles distributed over the eight
modules, each over five different time segments. The results are given in Table
12.3
and Fig.
12.9
(Ji et al. 2009a).
The mechanisms of interaction between TL and TR that are associated with the
nine modules appearing on the
x
-axis of Fig.
12.9
are listed in Table
12.4
. Since
there are three logical possibilities for the changes in TL and TR, namely, increase
(+), no change (0) or decrease (
5,184
¼
), there are a total of nine possible changes that can
be assigned to the combined system of TL and TR, and these possibilities are listed
