• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2519-2525
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• 2016

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

• Journal of Life Science
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• v.25 no.4
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• pp.376-384
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• 2015

To investigate the molecular events of controlling intramuscular fat (or marbling), which is an important factor in the evaluation of beef quality, we performed cDNA microarray analyses using the longissimus dorsi muscle and back fat tissues. For this study, we constructed normalized cDNA libraries: fat tissues in native Korean cattle (displaying 1,211 specific genes), and muscle tissues in native Korean cattle (displaying 1,346 specific genes). A bovine cDNA chip was constructed with 1,680 specific genes, consisting of 760 genes from muscle tissues and 920 genes from fat tissues. The microarray analysis in this experiment showed a number of differentially expressed genes, which compared the longissimus dorsi muscle (Cy5) with back fat tissue (Cy3). Among many specific differentially expressed genes, 12-lipoxygenase (oxidizing esterified fatty acids) and prostaglandin D synthase (differentiation of fibroblasts to adipocytes) are the key candidate enzymes that should be involved in controlling the accumulation of intramuscular fat. In this study, differentially and commonly expressed genes in the muscle and fat tissues of native Korean cattle were found in large numbers, using the hybridization assay. The expression levels of the selected genes were confirmed by semi-quantitative RT-PCR, and the results were similar to those of the cDNA microarray.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2007.11a
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• pp.149-152
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• 2007

본 논문은 바이오 인포메틱스의 분야를 간단히 소개하고 기능유전체학에서 microarray 실험에 대한 통계적 방법론을 살펴보고자 한다. 또한 DNA chip 설계와 생물학적 특정에 대해 살펴보고 각 분야에서 적용되는 통계적 방법을 연구분석 해보고자 한다.

• Proceedings of the Zoological Society Korea Conference
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• 2001.10a
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• pp.253.2-253
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• 2001

No Abstract, See Full Text

• Development and Reproduction
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• v.9 no.2
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• pp.65-83
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• 2005

The three important phases in the development of ligand immunoassays are identified and summarized. The competitive radiolabelled hormone measurement had been developed in the first and early in the second generations(1950s to 1960s), such as radioimmunoassays(RIA) or immunoradiometric(saturation) assays(IRMA), and used in all most of the hormone and also analyte in biological samples. In the second generation, ultrasensitive non-isotopic immunoassays(NIA) were developed using monoclonal antibodies(McAb), labelling the McAb and high specific activity non-isotopic labels. After their usefulness, advantages and disadvantages has been evaluated and non-competitive methods are discussed. The chip/microarray based multianalyte ligand assays(microspot or genechip methods) are developed and known as alternative ones in the third generation. We summarize the developments of NIAs and its usefulness, and then introduce briefly the new ligand assays.

• 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.

• Korean Journal of Medicinal Crop Science
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• v.15 no.2
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• pp.89-94
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• 2007

The effects of angiogenesis inhibitor from the extract libraries of Korean and Chinese medicinal plants were investigated using a protein microarray chip. Protein chip was constructed by immobilization of integrin ${\alpha}_5{\beta}_1$ on protein chip base plates and employed far screening active extracts that inhibit the integrin-fibronectin interaction from the extract libraries. The 100 extracts of medicinal plants were obtained from extract bank of National Institute of Crop Science, RDA. The 14 extracts among 100 extract libraries were shown efficient inhibition activity for the interaction between integrin-fibronectin. The medicinal plants of 14 extracts were Vitex negundo var. incisa (Lam.) C.B. Clarke, Epimedium koreanum Nakai, Cedrela sinensis A. Juss, Ipomea aquatica Forsk, Schisandra chinensis Baill, Pulsatilla koreana Nakai, Paeonia lactiflora Pall. var.hortensis Makino, Oenothera odorata, Allium chinense, Allium victorialis var. platyphyllum MAKINO, Polygonatum odoratum Druce var. pluriflorum Ohwi, Hosta lancifolia, Agrimonia pilosa L. var. japonica Nakai and Potentilla chinensis SER. The Paeonia lactiflora, Oenothera, and Agrimonia pilosa from these 14 extracts libraries were shown strong inhibition activity of integrin ${\alpha}_5{\beta}_1$.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2003.10a
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• pp.173-173
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• 2003

With the introduction of DNA microarrays, a high throughput analysis of gene expression is now possible as a replacement to the traditional time-consuming Southern-blot analysis. This cDNA microarray should be ahighly favored technology in the area of molecular toxicology or analysis of environmental stresses.In this study, therefore, we developed a novel cDNA microarray for analyzing stress-specific responses in japanese Medaka fish. In the design and fabrication of this stress specific functional cDNA microarray, 123 different genes in Medaka fish were selected from eighteen different stress responsive groups and spotted on a 25${\times}$75 mm glass surface. After exposure of the fish to bisphenol A which is the one of the well-known endocrine disrupting chemicals (EDCs), over 1 or 10 days, the responses of the DNA chip were found to show distinct expression patterns according to the mode of toxic actions from environmental toxicants. As a results, they showed specific gene expression pattern to bisphenol A, additionally, the chemical spesific biomarkers could be suggested based on the chip analysis data. Therefore, this chip can be used to monitor stress responses of unknown and/or known toxic chemicals using Medaka fish and may be used for the further development of biomarkers by utilizing the gene expression patterns for known contaminants.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.22-26
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• 2002

There are a number of ways in which environmental microbiology and microbial ecology will benefit from DNA micro array technology. These include community genome arrays, SSU rDNA arrays, environmental functional gene arrays, population biology arrays, and there are clearly more different applications of microarray technology that can be applied to relevant problems in environmental microbiology. Two types of the applications, bacterial identification chip and functional gene detection chip, will be presented. For the bacterial identification chip, a new approach employing random genome fragments that eliminates the disadvantages of traditional DNA-DNA hybridization is proposed to identify and type bacteria based on genomic DNA-DNA similarity. Bacterial genomes are fragmented randomly, and representative fragments are spotted on a glass slide and then hybridized to test genomes. Resulting hybridization profiles are used in statistical procedures to identify test strains. Second, the direct binding version of microarray with a different array design and hybridization scheme is proposed to quantify target genes in environmental samples. Reference DNA was employed to normalize variations in spot size and hybridization. The approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.

• KIEE International Transactions on Electrophysics and Applications
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• v.11C no.3
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• pp.85-90
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• 2001

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and other application area. So, the improvement of DNA detection system is very important for the determination of this hybridization reaction. In this study, we report the characterization of the probe and target oligonucleotide hybridization reaction using the evanescent field microscopy. First, we have fabricated DNA chip microarray. The particles which were immobilized oligonucleotides were arranged by the random fluidic self-assembly on the pattern chips, using hydrophobic interaction. Second, we have detected DNA hybridization reaction using evanescent field microscopy. The 5'-biotinylated probe oligonucleotides were immobilized on the surface of DNA chip microarray and the hybridization reaction with the Rhodamine conjugated target oligonucleotide was excited fluorescence generated on the evanescent field microscopy. In the foundation of this result, we could be employed as the basis of a probe olidonucleotide, capable of detecting the target oligonucleotide and monitoring it in a large analyte concentration range and various mismatching condition.