Molecular Array Experiments in which
biological materials are deposited onto a solid support at high density in
a known configuration (array targets). Labeled molecules are specifically
hybridized to the surface and detected. A specialized fluorescent scanner
and sophisticated data analysis software is usually required to get the
most out of the resulting data. The catalog of available pre made arrays
is growing rapidly, but there are plenty of applications for which no
suitable array can be found.
Some Types of Molecular
Arrays:
1- Oligo Expression Microarrays (DNA Chip,
Affymetrix),
2- cDNA Expression Microarrays (Cy dyes, Brown Lab,
Stanford U.),
3- Protein Arrays,
4- Macroarrays,
5-
CGH-Composition / Genomic Hybrids,
6- Methylation array,
7- Telomere
array,
8- Sequencing / Genoyping Arrays,
9- Tissue Arrays,
etc.
Some Expanded Definitions for Specific
Microarrays:
1- Oligonucleotide Microarrays
Do not
require the time-consuming cloning, isolation, and purification procedures
needed for cDNA-based approaches.
Shorter probes than in the cDNA
arrays (a stringent quality control is required).
Carefully chosen
oligonucleotides can enable researchers to distinguish between different
members of the same gene family, or even monitor single nucleotide
polymorphisms.
Cloning Artifacts can also be discovered after a careful
comparison of results within different species.
2- DNA
microarrays:
Glass microslides or nylon membranes containing DNA
samples (genomic DNA, cDNA, or oligonucleotides) in an ordered
two-dimensional matrix. Can be used to analyze gene expression and genomic
clones or to detect single nucleotide polymorphisms (SNPs).
In the
cDNA Microarrays the printed fragments are PCR products from a
library.
3- Macroarrays:
Without specialized microarray
instrumentation is possible to use membrane-based arrays. These arrays are
sometimes called "macroarrays" because their spot diameters are larger
than those achieved by microarrays.
Membrane-based arrays do not
generally require specialized instrumentation; instead, they employ
conventional hybridization and visualization techniques, such as
radioactive or chemiluminescent detection.
Properties Shared by
all Array Experiments:
1- Each sample has many variables measured,
2- Raw
data are image data,
3- Data are massive in
quantity,
Examples:
1- Many thousand genes in an
expression array,
2- All bands of a Chromosome in a
CGH array,
3- Many hundreds of epitopes in a protein
assay
Analysis of Array Data:
1- Identifying
differentially expressed genes (Means, ANOVA, Multiple testing, gene lists
and annotations, etc.)
2- Profile Analysis for expression pattern in
time courses
3- PCA (Principal Component Analysis),
4- Clustering
(can be done within or among different tissues),
5- Classification of
RNA sources,
6- Dendrograms within the results,
7- The Understanding
of Gene Function with Array Data is Elusive (other methodologies are
needed for that purpose).
Web Resources On Microarray
http://ihome.cuhk.edu.hk/~b400559/array.html
http://www.gene-chips.com/
http://www.nslij-genetics.org/microarray
Book Resources On Microarray
DNA
Microarrays and Gene Expression by Pierre Baldi, et al
Data
Analysis Tools for DNA Microarrays by Sorin Draghici
Microarrays
Methods and Applications: Nuts & Bolts by Gary Hardiman
Editor(s): Fernando Castro-Chavez