DNA Microarray Technology - DNA Microarray Technology and Data Analysis in Cancer Research - page 8

1.4. Interpretation of DNA Microarray Data
While expensive, DNA microarray experiments have not yielded suffi-
cient information that allows us to draw decisive conclusions. Often, what
we have in the end is a long list of more than 30 000 genes with fold
changes of their mRNA expression comparing control and experimental
groups. An easy explanation for the fold change of mRNA expression of
a particular gene, which is actually a way of obtaining information from
DNA microarrray data by most people, is that mostly changed genes in
expression are likely involved in the biological process being studied.
A “hot” list is often provided by statisticians to researchers to describe
which genes are mostly upregulated or downregulated, and those genes
with minor or no changes in mRNA expression are often considered as not
involved or not important by the researchers. However, there are numer-
ous examples showing a disassociation between the abundance of mRNA
and the level of translated protein for a gene of interest, and between the
abundance of mRNA and the effect of the gene of interest on a particular
biological process.
From our own experience, a general guess on the biological role of
a particular gene based on the fold change is sometimes agreeable to the
results of experiments testing the function of this gene, but it is not rare to
see misleading or wrong conclusions drawn based solely on the magni-
tude of the fold changes. Importantly, we learned that upregulation or
downregulation of a gene does not necessarily mean a positive or negative
role of this gene in the biological process being studied. A novel idea we
intend to propose here is that a gene with no change in its expression, as
determined by DNA microarray analysis, may still play a significant role
in the biological process. In Chapter 2, we describe in much more detail
and emphasize these ideas about the interpretation of DNA microarray
data, with specific examples from our own studies.
1.5. Advantages and Disadvantages
One of the biggest advantages of DNA microarray technology is that it can
evaluate simultaneously the relative expression of thousands of genes by
using small amounts of materials, providing gene signatures for particular