Castro-Chavez F. Microarrays, antiobesity and the liver. Annals of Hepatology 2004; 3(4): October-December: 137-145.

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