title: Characterization and simulation of cDNA microarray spots using a novel mathematical model.
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.
  
  
  CONCLUSIONS
  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.
authors: Department of Physiology, College of Medicine, Hanyang University, Seoul, 133-791, Korea. hykim121@hanyang.ac.kr
authors: Hye Young
authors: HY
authors: Kim
authors: Seo Eun
authors: SE
authors: Lee
authors: Min Jung
authors: MJ
authors: Kim
authors: Jin Il
authors: JI
authors: Han
authors: Bo Kyung
authors: BK
authors: Kim
authors: Yong Sung
authors: YS
authors: Lee
authors: Young Seek
authors: YS
authors: Lee
authors: Jin Hyuk
authors: JH
authors: Kim
mesh_terms: D003198:Computer Simulation; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D044085:Microfluidics / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods*; D008956:Models, Chemical; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity