• Proceedings of the Botanical Society of Korea Conference
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• 2002.04a
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• pp.104-104
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• 2002

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.98-107
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• 2006

Chromosomal copy number changes (aneuploidies) are common in human populations. The extra chromosome can affect gene expression by whole-genome level. By gene expression microarray analysis, we want to find aberrant gene expression due to aneuploidies in Klinefelter (+X) and Down syndrome (+21). We have analyzed the inactivation status of X-linked genes in Klinefelter Syndrome (KS) by using X-linked cDNA microarray and cSNP analysis. We analyzed the expression of 190 X-linked genes by cDNA microarray from the lymphocytes of five KS patients and five females (XX) with normal males (XY) controls. cDNA microarray experiments and cSNP analysis showed the differentially expressed genes were similar between KS and XX cases. To analyze the differential gene expressions in Down Syndrome (DS), Amniotic Fluid (AF)cells were collected from 12 pregnancies at $16{\sim}18$ weeks of gestation in DS (n=6) and normal (n=6) subjects. We also analysis AF cells for a DNA microarray system and compared the chip data with two dimensional protein gel analysis of amniotic fluid. Our data may provide the basis for a more systematic identification of biological markers of fetal DS, thus leading to an improved understanding of pathogenesis for fetal DS.

• Journal of Acupuncture Research
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• v.20 no.3
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• pp.34-44
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• 2003

Objective : Bone homeostasis is maintained by balance of bone formation and resorption. Therefore, bone related diseases arose by disturbance of this balance between osteoblast and osteoclast activities. To develop a successful screening system the therapeutic components based on oriental medicine is essential to set up systematic approach for that purpose. The purpose of this study is to the know the gene expression using cDNA microarray assay. Methods : Cervi Pantotricuhum Cornu Herbal-acupuncture extract was prepared by boiling. human osteosarcoma cells(HOS) were treated with Cervi Pantotricuhum Cornu Herbal-acupuncture solution. Then mRNA was extracted and cDNA microarray assay was performed. Results : Human osteosarcoma cells(HOS) treated with Cervi Pantotricuhum Cornu Herbal-acupuncture solution($500{\mu}g/m{\ell}$) showed that thioredoxin, TAFII31 and two novel genes were increased. However many genes decreased their expression by Cervi Pantotricuhum Cornu Herbal-acupuncture. Conclusions : This type of approach will give a good chance to explore the favorable effects of Cervi Pantotricuhum Cornu Herbal-acupuncture. Further study is needed for investigating the effect of Cervi Pantotricuhum Cornu Herbal-acupuncture.

• Journal of KIISE:Software and Applications
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• v.29 no.11
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• pp.775-784
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• 2002

Microarray data, obtained from DNA chip technologies, is the measurement of the expression level of thousands of genes in cells or tissues. It is used for gene function prediction or cancer diagnosis based on gene expression patterns. Among diverse methods for data analysis, the Bayesian network represents the relationships among data attributes in the form of a graph structure. This property enables us to discover various relations among genes and the characteristics of the tissue (e.g., the cancer type) through microarray data analysis. However, most of the present microarray data sets are so sparse that it is difficult to apply general analysis methods, including Bayesian networks, directly. In this paper, we harness an efficient structural learning algorithm and data dimensionality reduction in order to analyze microarray data using Bayesian networks. The proposed method was applied to the analysis of real microarray data, i.e., the NC160 data set. And its usefulness was evaluated based on the accuracy of the teamed Bayesian networks on representing the known biological facts.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.7
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• pp.933-941
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• 2005

To develop a functional cDNA chip, specific genes expressed in the tissues of swine Kagoshima Berkshire were screened. A total of 4,434 ESTs were obtained by constructing a cDNA library from total RNA isolated from the muscle and fat tissues, affirming their functions by investigating similarity of nucleotide sequences with the database at the NCBI. Among them, 1,230 ESTs were confirmed as novel genes, which, to date, have not been identified. Attaching the genes to a cDNA microarray slide revealed expression patterns of genes in muscle and fat according to the growth stages of swine. As specific genes expressed in the muscle tissues of swine with body weight of 30 kg, 60 genes including actin, myosin, tropomysin, transfer RNA-trp synthetase, Kel-like protein 23, KIAA0182 and COI, Foocen-m, etc were obtained. In addition, 18 novel genes were obtained. As specific genes expressed in fat tissues of swine with body weight of 30 kg, 47 genes including annexin II, Collagen, Fibronectin, Pleckstrin homology domain, serine protease, etc were obtained. 21 novel genes were also obtained. The genes specifically expressed in the muscle and fat tissues of swine affect contraction and relaxation of the muscle and the fat. However, studies on the expression mechanisms of the genes are insufficient. To reveal species of structural genes in swine muscle and fat tissue, interrelation studies in expression and function of genes by using the cDNA chip should be conducted.

• The Journal of the Korean Society for Microbiology
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• v.35 no.4
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• pp.299-308
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• 2000

Recently developed cDNA microarray or DNA chip technology allows expression monitoring of expression of hundreds and thousands of genes simultaneously and provides a format for identifying genes as well as changes in their activity. In order to search for changes in gene expression after X irradiation in HL60 cells, cDNA microarray technique was done. In this study, expression of 588 human genes (including oncogenes, tumor suppressor genes, cell cycle regulator genes, intracellular signal transduction modulator genes, apoptosis related genes, transcription factor genes, growth factors and receptor genes, cytokine genes, etc) were analyzed. For cDNA microarray analysis mRNAs were extracted from control and 8 Gy-irradiated HL60 cells. As a result the changes in expression of several genes were observed. This alteration of gene expression was confirmed by reverse transcription-polymerase chain reaction. The expression of heat shock 60 KD protein, c-jun, erythroid differentiation factor, CPP32, myeloid cell nuclear differentiation antigen, MAP kinase-activated protein kinase, interleukin-8, monocyte chemotactic peptide 1 and RANTES genes was increased, but the expression of p55CDC gene was decreased after X irradiation.

• Journal of Microbiology and Biotechnology
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• v.10 no.1
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• pp.21-26
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• 2000

A microarrayer system was developed mainly for manufacturing DNA chips. The 3-axis robot was designed to automatically collect samples from 96-or 384-well microtiter plates using up to 16 simultaneously moving pens and to deposit them on a surface-modified slide glass. This is followed by a wash/dry operation in a clean station. The cycle is repeated with a new set of samples, This system can deposit cDNA or oligonucleotides with spot intervals of $150{\;}\mu\textrm{m}$ and the spot size of $80\mu\textrm{m}$, thus allowing a high density DNA chip containing about 5,000 spots per $\textrm{cm}^2$. The entire procedure is controlled by the Visual C++ program that was written in our laboratory by using a personal computer with Pentium 100 CPU.

• Proceedings of the Korean Society of Toxicology Conference
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• 2002.05a
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• pp.81-81
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• 2002

The recent development of cDNA microarray or cDNA chip technology has made it possible to analyze the expression of thousands of genes at once. In present study, we made radioresistant clones (#1 and #4) from NIH3T3 cells which are not tumorigenic and we identified 4 genes using microarray system, cdk6, cdc25B, mdm-2 and nidogene, which were altered in radiaiton resistanct NIH3T3 cells.(omitted)

• Molecules and Cells
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• v.22 no.3
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• pp.254-261
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• 2006

DNA microarray is a powerful tool for high-throughput analysis of biological systems. Various computational tools have been created to facilitate the analysis of the large volume of data produced in DNA microarray experiments. Normalization is a critical step for obtaining data that are reliable and usable for subsequent analysis such as identification of differentially expressed genes and clustering. A variety of normalization methods have been proposed over the past few years, but no methods are still perfect. Various assumptions are often taken in the process of normalization. Therefore, the knowledge of underlying assumption and principle of normalization would be helpful for the correct analysis of microarray data. We present a review of normalization techniques from single-labeled platforms such as the Affymetrix GeneChip array to dual-labeled platforms like spotted array focusing on their principles and assumptions.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.30 no.3C
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• pp.112-118
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• 2005

In this paper, we propose a new nonlinear matching measure for automatic analysis of the on-off type DNA microarray images in which the hybridized spots are detected by the template matching method. The proposed measure is obtained by binary-thresholding over the whole template region and taking the number of white pixels inside the spotted area. This measure is compared with the normalized covariance in terms of the classification ability of the successfulness of the locating markers. The proposed measure is evaluated for the scanned images of HPV DNA microarrays where the marker locating is a critical issue because of the small number of spots. The targeting spots of HPV DNA chips are designed for genotyping 22 types of the human papilloma virus(HPV). The proposed measure is proven to give more discriminative response reducing the miss cases of the successful marker locating.