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which was followed by a smaller decrease (12%) between 450 and 850 minutes.
In contrast, the
TR
values averaged over 5,753-5,829 genes exhibited very differ-
ent kinetic behaviors: A rapid increase by about 60% during the first 5 minutes
followed by a 150% decrease to the 10% level of the control by 120 minutes.
This low level of
TR
was maintained until 360 minutes when it started to increase
linearly up to the 45% level of the control by 850 minutes. The
TL
and
TR
val-
ues were normalized with respect to their values at t = 0, and corrected for the
increasing number of cells during the observational period.
These observations clearly indicate that the average
TL
and
TR
values do not
change in parallel (as would have been expected if
TL
reflected the rates of gene
expression, namely
TR
) but exhibit seemingly
independent
kinetic behaviors, es-
pecially during the first (0-5 minutes) and the last (450 - 850 minutes) periods of
observation. The relation between
TL
and
TR
can be visualized by plotting
TL
against
TR
on a 2-dimensional plane as shown in Fig. 12.1a through 12.1d. A
trajectory in the
TR
versus
TL
plane consists of a set of 5 vectors, each represent-
ing the change in
TL
and
TR
over a time interval which varies from 5 minutes to
400 minutes. The trajectory associated with the gene YBL091C-A consists of a
series of five connected vectors starting from time point 1 (0 minute) and ending
at time point 6 (850 minutes) having approximate angles of 315
◦
,
270
◦
,
135
◦
,
45
◦
,
and 45
◦
. A given vector is associated with a mechanism of RNA metabolism ex-
pressedintermsof
TL
and
TR
. Specifically, when
α
= 315
◦
, it indicates that,
during the first time interval (
i.e.
, from 0 to 5 minutes), the transcript level
TL
of gene TBL091C-A is increased but its transcription rate
TR
is decreased; when
α
= 270
◦
, it indicates that the same gene experienced no change in
TL
but a de-
crease in
TR
,
etc
. It is important to note that this gene experienced an increase in
both
TL
and
TR
only during the last two time intervals, since their associated
α
values are approximately 45
◦
. The 9 mechanisms of RNA metabolism depicted
in Fig. 12.2 are defined as follows:
(1)
Mechanism 1
is definedbythe
α
values ranging from 357
◦
(or
3
◦
)to
−
3
◦
and indicates that
TL
increases without any change in
TR
;
(2)
Mechanism 2
is defined by the
α
values ranging from 3
◦
to 87
◦
and
indicates that both
TL
and
TR
increase;
(3)
Mechanism 3
is defined by the
α
values ranging from 87
◦
to 93
◦
and
indicates that
TL
does not change although
TR
increases;
(4)
Mechanism 4
is defined by the
α
values ranging from 93
◦
to 177
◦
and
indicates that
TL
decreases even though
TR
increases;
(5)
Mechanism 5
is definedbythe
α
values ranging from 177
◦
to 183
◦
and
indicates that
TL
decreases without any change in
TR
;
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