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

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 o...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong-Sung Lee, Young Seek Lee, Jin Hyuk Kim
• Keywords: BMCBI 2007, CDNA, CDNA Deposition, CDNA Microarray