Gene expression microarrays

cDNA microarray image segmentation using root signals

“…Complementary deoxyribonucleic acid (cDNA) microarray imaging ( Fig. 1) is considered one of the most important and powerful technologies used to extract and interpret genomic information (Arena et al, 2002;Whitchurch, 2002;Zhang et al, 2002). Analysis of cDNA microarray data helps in monitoring the expression levels of thousands of genes simultaneously (Eisen and Brown, 1999;Nagarajan and Upreti, 2006) and provides information relevant to cell activity (Damiance et al, 2004).…”

“…2) requires first to isolate ribonucleic acid (RNA) from both control and experimental sample. In the sequence, the extracted RNAs are converted into cDNAs by the so-called reverse transcription process (Whitchurch, 2002). Using a Cy3/Cy5 system (Nagarajan, 2003), the procedure continues by labeling the cDNAs with fluorescent probes, usually Cy3 for the control and Cy5 for the experimental channel.…”

“…The image spots' coloration represents the abundance of hybridized RNA in the array (Whitchurch, 2002;Lukac et al, 2004b). The presence of RNA from the experimental (test) or control (reference) population of cells is determined by the red or green spots, respectively.…”

“…Based on this simple coloration concept, cDNA microarray based gene expression analysis uses the measurement of the hybridized RNA abundance as a measure of gene expression activity (Katzer et al, 2003). The vast amount of data and calculations needed to obtain the relative expression levels of the genes from the fluorescence intensity at each spot necessitates the development of automated data processing solutions (Filkov et al, 2002;Whitchurch, 2002). Since a number of impairments 2 may affect the cDNA microarray image formation, image processing is necessary in order to eliminate processing errors from propagating further down the processing pipeline to the gene expression analysis tasks (Zhang et al, 2002;Istepanian, 2003;Lukac et al, 2004b).…”

A Data-Adaptive Approach to cDNA Microarray Image Enhancement

“…The two channels are combined to form the cDNA vector x (r,s) in a two-dimensional vector space [2,5]. Thus, the microarray data form a two-channel, Red-Green (RG) image [9,10].…”