A DNA microarray consists of an orderly arrangement of DNA, cDNA, or oligonucleotide probes that represent individual genes of an organism. Today, microarrays are the most important tools used to analyze gene transcription on a large scale. Investigations reach from finding key genes in whole genomes to looking at overall patterns of gene expression. This provides a better understanding of the architecture of genetic regulatory networks and helps to identify those genes in the genome that are differentially expressed, e.g., during cellular programs, in tumors or as the result of a treatment. The use of different fluorescent dyes allows mRNAs from two different sources (tissues, strains, or differently treated cells) to be labeled in different colors, mixed, and hybridized to the same array, which results in competitive binding of the target to the arrayed sequences. After hybridization and washing, the slide is scanned using two different wavelengths corresponding to the dyes used, and the intensity of the same spot in both channels is compared. This results in a measurement of the ratio of transcript levels for each gene represented on the array. In order to find significantly regulated genes, the resulting data are analyzed by different bioinformatic tools such as R and significance analysis of microarrays (SAM).