Gene Array Analysis

Gene array analysis is a method to simultaneously evaluate the expression of many genes. It can be used for sequence identification such as mutation analysis as well. Gene arrays are solid surfaces, such as a microscope slide, on which a number of nucleotide sequences belonging to a gene have been placed at defined locations by spotting or by direct synthesis. The aim of using this technology is to recognize the existence and abundance of labeled nucleic acids in a biologic sample, which is hybridized to the nucleotide sequences on the gene array. This technology is a very young one and is growing very fast. One of the most important features of gene arrays is the amount of quantitative data they can provide. The major challenge for using this technology is the methods that can be used for dealing with such a huge amount of data. These data can be interpreted in different ways. Bioinformatics is capable of helping to interpret the data provided by gene arrays by using mathematics, statistics, and computer science technology. In other words, gene array analysis is the analysis of data provided by gene arrays to obtain the correct interpretations and significant results.

The nucleic acids attached to the array or the labeled nucleic acid of the sample are called target, while the labeled nucleic acids compromising the sample are called probes. The amount of probe hybridized to each target spot provides information about specific nucleic acid composition of the sample. A gene array experiment has the advantage of getting the information on thousands of targets in a single experiment.

There are different kinds of gene arrays including nylon membrane arrays, glass slide arrays, and affymetrix's gene chips.

There are several terms that are used to refer to gene arrays including biochip, DNA chip, GeneChip® (Affymetrix, Inc.), DNA array, microarray, and macroarray. In general, biochip, DNA chip, or GeneChip refers to gene arrays on glass slides. Microarray and macroarray indicate the spot size or the number of spots on the slide.

Gene arrays are powerful tools to compare complex sample RNA populations. For example, using array analysis, the expression profiles of normal and tumor tissues, treated and untreated cell cultures, developmental stages of an organism or tissue, and different tissues can be compared. A typical gene array experiment involves the following:

• 1.
  Isolating RNA from the samples to be compared;
• 2.
  Converting the RNA samples to labeled cDNA via reverse transcription;
• 3.
  Hybridizing the labeled cDNA to identical membrane or glass slide arrays;
• 4.
  Removing the unhybridized cDNA;
• 5.
  Detecting and quantization the hybridized cDNA; and
• 6.
  Comparing the quantitative data from the various samples.

For validating the differences in expression of special genomic sequences, another method of analysis, such as RT-PCR, Northern analysis, or nuclease protection assays, is used. These procedures can be used for relative or absolute quantization of specific data recognized by gene array analysis. The most challenging part of a gene array experiment is the data analysis, which is performed with the help of computer and bioinformatics. Just one gene array experiment can offer thousands of data points. Then, making sense of the provided data is of great importance.

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