Whole Cells - Molecular Theory of the Living Cell - page 394

Table 12.2 The multiple meanings of “gene expression” depending on context
Meaning of
“gene expression” Context of experiment

1. RNA level 1. Usual microarray experiments

2. Transcription 2. Microarray experiment using the “genomic run- on” protocol

3. Protein level 3. Protein microarrays

4. Pathway activation 4. Microarrays prepared with cDNAs encoding metabolic pathways

5. Cell morphology
or properties

5. Microarrays designed to bind cell surface proteins characteristic
of cell morphology

The mRNA levels in control and test samples are ... compared and the differential
expression data given as a ratio or fold change . (Okamoto 2005) (12.9)
These statements would be correct if the term “genes” (in bolds) are replaced
by “RNA levels” or “transcripts.” This is simply because:
DNA microarrays, as normally used, measure RNA levels but not the rates of transcription.
(12.10)

The phrase “gene expression” in the context of usual microarray experiments
necessarily signifies “transcription” or Step 1 in Fig. 12.5 . In other contexts, “gene
expression” canmean transcription rate , protein , metabolism, morphology, or any other
phenotypes being measured (see Table 12.2 ). In particular, if (and only if) microarrays
are used in conjunctionwith the genomic run-on protocol (Garcia-Martinez et al. 2004),
does “gene expression” mean “transcription” (see Row 2 in Table 12.2 ).
We commonly read Statement 12.11 in journal articles and advertisements or
hear in seminars and lectures all over the world:
Microarrays measure gene expression.

(12.11)

Statement 12.11 can be true but not always so, since the phrase “gene expression”
can mean any of the five different objects listed in the first column of Table 12.2 ,
depending on the context of the experiment performed, leading to the following
conclusion:

The meaning of “gene expression” cannot be determined without knowing the experimental
protocol employed in microarray experiments. (12.12)
The critical dependence of the meaning of gene expression on protocol as
embodied in Statement 12.12 can be represented diagrammatically utilizing the
triadic definition of a sign given by Peirce (see Sect. 6.2.1 ) (Fig. 12.7 ):
Combining Statements 12.11 and 12.12 leads to:
Microarrays can measure any one of at least five different observables, including transcript
levels and transcription rates, depending on the experimental protocol employed.

(12.13)

A corollary of Statement 12.13 is:
Microarrays cannot measure both transcript levels (TL) and transcription rates (TR)
without using two independent experimental protocols. (12.14)

To many investigators who utilize microarrays, Statements 12.10 and 12.14 may
come as a surprise because microarrays have been widely advertised in journals and