Basic Applied Bioinformatics

CHAPTER 39Overview of Microarray Data Analysis

RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

39.1 CONCEPT

Microarray technology is used to study the expression of many genes at a time, which is the simultaneous detection of many genes. Thousands of gene sequences (called probes) are placed on a glass slide (called a gene chip), and a sample containing DNA or RNA or protein (depending upon the types of microarray) called “probes” is placed in contact with gene chip. Hybridization occurs between targets and probes, and produces light that is measured and quantifed.

39.2 GETTING STARTED WITH MICROARRAY

The principle of microarray has been used in different areas of molecular biology (Source: Wikipedia), including: DNA microarrays (cDNA, oligonucleotide microarrays, SNP‐chip); MMChips (microRNA); Protein‐microarrays; Reverse Phase Protein Microarrays; Tissue‐microarrays; Chemical compound microarrays; Antibody microarrays; Carbohydrate arrays (glycoarrays), and so on.

These different types of microarray are spotted arrays on glass, self‐assembled arrays and in situ synthesized arrays. There are two types of experimental procedures, and they are either one‐color or two‐color approaches. In the one‐color approach, a sample is labeled singly with either Cy3 or Cy5 fluorophore, and hybridized to a single microarray chip. In the two‐color microarray, two samples (usually sample and reference) are labeled with two different fluorophores (Cy3 and Cy5), and are hybridized ...