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Characterization and simulation of cDNA microarray spots using a novel mathematical model.

Kim HY, Lee SE, Kim MJ, Han JI, Kim BK, Lee YS, Lee YS, Kim JH - BMC Bioinformatics (2007)

Bottom Line: The morphology of the resulting cDNA deposit can be classified into three types: a doughnut shape, a peak shape, and a volcano shape.With the results of the simulation and the parameter estimation, the phenomenon of the formation of cDNA deposits in each type was investigated.We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physiology, College of Medicine, Hanyang University, Seoul, 133-791, Korea. hykim121@hanyang.ac.kr

ABSTRACT

Background: The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been suggested to increase the accuracy of microarray gene expression data, it is necessary to obtain reliable microarray images by improving wet-lab experiments. As the first step of a cDNA microarray experiment, spotting cDNA probes is critical to determining the quality of spot images.

Results: We developed a governing equation of cDNA deposition during evaporation of a drop in the microarray spotting process. The governing equation included four parameters: the surface site density on the support, the extrapolated equilibrium constant for the binding of cDNA molecules with surface sites on glass slides, the macromolecular interaction factor, and the volume constant of a drop of cDNA solution. We simulated cDNA deposition from the single model equation by varying the value of the parameters. The morphology of the resulting cDNA deposit can be classified into three types: a doughnut shape, a peak shape, and a volcano shape. The spot morphology can be changed into a flat shape by varying the experimental conditions while considering the parameters of the governing equation of cDNA deposition. The four parameters were estimated by fitting the governing equation to the real microarray images. With the results of the simulation and the parameter estimation, the phenomenon of the formation of cDNA deposits in each type was investigated.

Conclusion: This study explains how various spot shapes can exist and suggests which parameters are to be adjusted for obtaining a good spot. This system is able to explore the cDNA microarray spotting process in a predictable, manageable and descriptive manner. We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays.

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Related in: MedlinePlus

Changes in inner diameter of doughnut-shaped spot. The default values of the parameters were set as x0 = 1000, K = 0.002, a = 0.4, and KV = 3. By decreasing the value of each parameter with 20 steps and fixing the other four parameters with the default values, we obtained 20 variously shaped spots and measured the inner diameters of the spots. The decrements of x0, K, a, and KV were set as 35, 7.5E-5, 0.04, and 0.1, respectively. The inner diameter was measured at the height of half of the maximum intensity.
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Figure 5: Changes in inner diameter of doughnut-shaped spot. The default values of the parameters were set as x0 = 1000, K = 0.002, a = 0.4, and KV = 3. By decreasing the value of each parameter with 20 steps and fixing the other four parameters with the default values, we obtained 20 variously shaped spots and measured the inner diameters of the spots. The decrements of x0, K, a, and KV were set as 35, 7.5E-5, 0.04, and 0.1, respectively. The inner diameter was measured at the height of half of the maximum intensity.

Mentions: The doughnut-shaped spot was defined as the spot having a thin rim of high density of deposited cDNA and a large hole of very low density, approximated to zero (Figure 4a, left and middle). The diameters of the inner hole of the doughnut-shaped spots were measured by varying the parameters. Histograms of the density of deposited cDNA were bimodal, which had a peak at zero (Figure 4a, right). If the inner hole is included in measuring the signal, then there will be a discrepancy between the measures and the true value. To verify which parameter can influence the morphology of the doughnut-shaped spot, we changed each parameter by 20 steps while the others were fixed. The inner hole was decreased by increasing a, and KV and decreasing x0 and K (Figure 5).


Characterization and simulation of cDNA microarray spots using a novel mathematical model.

Kim HY, Lee SE, Kim MJ, Han JI, Kim BK, Lee YS, Lee YS, Kim JH - BMC Bioinformatics (2007)

Changes in inner diameter of doughnut-shaped spot. The default values of the parameters were set as x0 = 1000, K = 0.002, a = 0.4, and KV = 3. By decreasing the value of each parameter with 20 steps and fixing the other four parameters with the default values, we obtained 20 variously shaped spots and measured the inner diameters of the spots. The decrements of x0, K, a, and KV were set as 35, 7.5E-5, 0.04, and 0.1, respectively. The inner diameter was measured at the height of half of the maximum intensity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2267720&req=5

Figure 5: Changes in inner diameter of doughnut-shaped spot. The default values of the parameters were set as x0 = 1000, K = 0.002, a = 0.4, and KV = 3. By decreasing the value of each parameter with 20 steps and fixing the other four parameters with the default values, we obtained 20 variously shaped spots and measured the inner diameters of the spots. The decrements of x0, K, a, and KV were set as 35, 7.5E-5, 0.04, and 0.1, respectively. The inner diameter was measured at the height of half of the maximum intensity.
Mentions: The doughnut-shaped spot was defined as the spot having a thin rim of high density of deposited cDNA and a large hole of very low density, approximated to zero (Figure 4a, left and middle). The diameters of the inner hole of the doughnut-shaped spots were measured by varying the parameters. Histograms of the density of deposited cDNA were bimodal, which had a peak at zero (Figure 4a, right). If the inner hole is included in measuring the signal, then there will be a discrepancy between the measures and the true value. To verify which parameter can influence the morphology of the doughnut-shaped spot, we changed each parameter by 20 steps while the others were fixed. The inner hole was decreased by increasing a, and KV and decreasing x0 and K (Figure 5).

Bottom Line: The morphology of the resulting cDNA deposit can be classified into three types: a doughnut shape, a peak shape, and a volcano shape.With the results of the simulation and the parameter estimation, the phenomenon of the formation of cDNA deposits in each type was investigated.We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physiology, College of Medicine, Hanyang University, Seoul, 133-791, Korea. hykim121@hanyang.ac.kr

ABSTRACT

Background: The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been suggested to increase the accuracy of microarray gene expression data, it is necessary to obtain reliable microarray images by improving wet-lab experiments. As the first step of a cDNA microarray experiment, spotting cDNA probes is critical to determining the quality of spot images.

Results: We developed a governing equation of cDNA deposition during evaporation of a drop in the microarray spotting process. The governing equation included four parameters: the surface site density on the support, the extrapolated equilibrium constant for the binding of cDNA molecules with surface sites on glass slides, the macromolecular interaction factor, and the volume constant of a drop of cDNA solution. We simulated cDNA deposition from the single model equation by varying the value of the parameters. The morphology of the resulting cDNA deposit can be classified into three types: a doughnut shape, a peak shape, and a volcano shape. The spot morphology can be changed into a flat shape by varying the experimental conditions while considering the parameters of the governing equation of cDNA deposition. The four parameters were estimated by fitting the governing equation to the real microarray images. With the results of the simulation and the parameter estimation, the phenomenon of the formation of cDNA deposits in each type was investigated.

Conclusion: This study explains how various spot shapes can exist and suggests which parameters are to be adjusted for obtaining a good spot. This system is able to explore the cDNA microarray spotting process in a predictable, manageable and descriptive manner. We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays.

Show MeSH
Related in: MedlinePlus