Genomics refers to the comprehensive study of genes and their
function. Recent advances in bioinformatics and high-throughput
technologies such as microarray analysis are bringing about a
revolution in our understanding of the molecular mechanisms underlying
normal and dysfunctional biological processes. Microarray studies
and other genomic techniques are also stimulating the discovery
of new targets for the treatment of disease which is aiding drug
development, immunotherapeutics and gene therapy. In this site,
we have compiled an extensive list of resources to assist reseachers
interested in establishing a microarray platform and performing
expression profiling experiments.
Gene expression profiling or microarray analysis has enabled
the measurement of thousands of genes in a single RNA sample.
There are a variety of microarray platforms that have been developed
to accomplish this and the basic idea for each is simple: a glass
slide or membrane is spotted or "arrayed" with DNA
fragments or oligonucleotides that represent specific gene coding
regions. Purified RNA is then fluorescently- or radioactively
labeled and hybridized to the slide/membrane. In some cases,
hybridization is done simultaneously with reference RNA to facilitate
comparison of data across multiple experiments. After thorough
washing, the raw data is obtained by laser scanning or autoradiographic
imaging (Figure 1). At this point, the data may then be entered
into a database and analyzed by a number of statistical methods.
A number of issues must be addressed before establishing a
microarray platform and beginning expression profiling studies,
in particular, the overall cost. For a cDNA microarray platform,
one must purchase a clone set, robot, printing pins and the reagents
needed for DNA amplification and purification. The cost of these
materials can vary significantly, but one can expect to need
at least $100,000 to establish such a platform. However, once
the process of printing and hybridizing microarrays has been
optimized, the cost per experiment will fall dramatically. Thus,
one must decide if the number of planned experiments is enough
to warrant the time and cost of establishing a microarray platform.
If not, it may be more prudent to seek the services of an academic
microarray core facility or a commercial entity.
This website is organized into five major categories, each
representing different steps of the expression profiling process.
Links to useful PROTOCOLS are
provided that succinctly describe the microarray process from
DNA amplification to array scanning. These protocols encompass
the most commonly used microarray platforms which include cDNA
arrays, membrane arrays and Affymetrix gene chips. Also provided
on this site are links to specific manufacturers of the INSTRUMENTS
required to develop a microarray platform including robots and
scanners. The SOFTWARE section
of this site includes links to powerful academic and commercial
programs that are useful for managing microarray data and analyzing
results. Also contained within this site are links to microarray
DATABASES, some of which serve
as public data repositories and others that may be mined for
gene expression data. Finally, the VALIDATION
section includes a set of links that direct viewers to quantitative
"real time" PCR resources. These include primer design
programs, real time PCR primer set databases, and commercial
instruments, kits and services. Collectively, these resources
will greatly assist researchers in finding information related
to gene expression profiling.
If you are relatively new to the microarray field, we have
provided a list of literature references below that describe
in detail the process of designing and performing gene expression
profiling experiments. In addition, links to several discussion
groups are provided in order to facilitate the process of gathering
information in the microarray field.
Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes
JE, Snesrud E, Lee N, Quackenbush J (2000) A concise guide to
cDNA microarray analysis. Biotechniques 3, 548-554.
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative
monitoring of gene expression patterns with a complementary DNA
microarray. Science 270, 368-371. [PUBMED]
Microarray Discussion boards