Design and development of an automated system for the determination of gene expression ratios using DNA microarray images

Abstract

DNA Microarray chips enable scientists to investigate and explore critical biological newlineproblems on a genomic scale. This technology helps researchers to track thousands newlineof gene expression ratios systematically and thoroughly in a single experiment. In a newlinemicroarray experiment, the relative abundance of the spotted DNA sequences can be newlineestimated using differential hybridization of the two samples (normal and diseased) newlinethat draw meaningful biological conclusions. This is called the gene expression newlineratio or simply gene expression. After this competitive hybridization, the DNA chip newlineis photographed with an image scanner. As a result, two 16-bit tagged microarray newlineimages (MAIs) in TIFF (.tif) file format are produced, one for each (normal and newlinediseased), representing the findings of the microarray experiment. To distinguish the newlinesamples, two fluorescent dyes, green dye named Cy3 (570 nm) for normal and red newlinedye Cy5 (670 nm) for diseased, are tagged, respectively. Thus a pair of monochrome newlinemicroarray images have been obtained for the green and red channels. MAI has newlinebeen chiefly employed in genetic research, disease analysis, and drug discovery since newline1995. newlineTypically, an MAI contains subgrids or sub-arrays of orderly arranged gene newlineprobes called spots. Spots make up the foreground region of the microarray image, newlinewhich is set against a vast dark background. Every single spot contains the independent newlinegene information. DNA/cDNA Microarray Image Analysis (DNA/cDNA-MIA) newlineis an inevitable area of microarray experimental research studies that could theoretically newlinehave a significant influence on subsequent analyses, namely clustering or newlinedifferential gene detection.The following are the major steps involved in the analysis newlineof a genuine cDNA-MIA. 1) Image enhancement, 2) Gridding of sub-arrays and newlinespots, 3) Segmentation of spots, 4) Correction of background intensities around spots,5) Flagging of spurious or noisy spots from segmented spots, 6) Extraction of gene newlineintensities of spots, and 7) Examination of gene expressions. newline