Information Technology Reference
In-Depth Information
Fig. 6.2
Microarray experiment
There are basically two types of DNA microarrays: high-density oligonu-
cleotide (HDO) arrays and complementary DNA (cDNA) microarrays. HDO
microarrays provide high-quality spots of short sequences of 20-50 oligonu-
cleotides length, which are arranged on the carrier material in extreme density.
These arrays are comparatively expensive, but allow for the identification of
absolute quantities of hybridized RNA. Note that market leader Affymetrix
calls its HDO microarrays
GeneChips
, and this term is also frequently used
in literature. The spots of cDNA microarrays consist of longer cDNA probes,
which are hybridized with the differently labeled (red and green dyes) cDNA
probes of two cell populations. The resulting two-color spotted cDNA mi-
croarrays only allow for the identification of relative quantities, but they are
more economical than HDO microarray experiments. Similarly, protein ar-
rays are used in proteomics (another sub-discipline of Systems biology) for
the simultaneous functional analysis of proteins.
A proper experimental design is crucial for microarray experiments in order
to minimize systematic errors,suchas measurementdeviations due to incorrect
instrument calibrations or changing environment conditions. However, also for
well-performed experiments, the analysis of the results (mostly based on the
detected spot intensities) is again complex, as detailed in the next section.
6.1.2 Microarray Data Analysis
The very first step in the interpretation of data from microarray experiments
is the analysis of the produced displays, that is, the measuring of the spots'
intensities and their conversion into numerical values. This demanding image
processing task (spots have to be identified unambiguously) is usually carried
out by the specialized software of a microarray scanner, so that the researcher
starts the actual, specific data analysis based on the spot intensities and
possibly available meta-data. The preprocessing and differential expression
Search WWH ::
Custom Search