Biology Reference
In-Depth Information
Table 12.6 The “ribonic matrix” for characterizing cell state. P
i
¼
the ith
pathway,
where i runs
from 1 to n, where n is ~200 in budding yeast; R
j
¼
the jth
RNA molecule,
where j runs from 1 to
m, where m is ~6,300 in budding yeast; N
i
the ith
node number
defined in Fig.
12.12
, where i
runs from 1 to r
2
where r is the linear size of the principal grid;
a
/m
¼
the average number of RNA
molecules participating in a metabolic pathway, where
a
is the sum of the numbers in the last row
and m is the number of the RNA molecules with known functions, and
b
is the sum of the numbers
appearing in last column, and
b
/m is the average number of the metabolic functions carried out by
an RNA molecule in budding yeast
Cell type X, perturbation Y
¼
Metabolic pathways (n)
RNA molecules with
known functions (m)
Number of metabolic roles
played by an RNA (
m
)
P
1
P
2
P
3
P
n
...
R
1
N
1
-
-
7
2
R
2
N
5
N
7
-
-
2
R
3
-
99
-
1
R
4
N
7
-
25
-
2
R
5
N
3
-
-
100
2
.
.
.
R
m
N
7
-
55
N
6
3
...
Number of RNAs encoding
a pathway (
e
)
5
2
2
2
b
a
mathematics of principal component analysis such as ViDaExpert (Sect.
12.8.1
)
will give rise to what is here called “RNA spectroscopy” or more briefly
“ribonoscopy” as indicated in Eq.
12.21
and exemplified in Fig.
12.12
. Finally,
just as the interpretation of molecular spectra requires applying the concepts, laws,
and principles of
quantum mechanics
, so the correct interpretation of ribonic
spectra is predicted to require applying a
comprehensive molecular theory of the
living cell
, such as the one developed in this topic:
Ribonoscopy
¼
DNAMicroarrays
þ
PrincipalComponentAnalysis
ð
implemented by
;
e
:
g
:;ViDaExpertÞ
(12.21)
The practical applications of
ribonoscopy
in pharmaceutical science and medi-
12.8.3
Ribonics
: The Study of Ribons with Ribonoscopy
The
ribonic spectra
of metabolic pathways, some examples of which are being
shown in Fig.
12.12
, can be analyzed in a tabular form, to be referred to as the
“ribonic matrix” (see Table
12.6
). The rows in the table represent
m
different RNA
