• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.08a
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• pp.77-102
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• 2001

Different high-throughput chip technologies are available for genome-wide gene expression studies. Quality control and prescreening analysis are important for rigorous analysis on each type of gene expression data. Statistical significance evaluation of differential expression patterns is needed. Major genome institutes develop database and analysis systems for information sharing of precious expression data.

• KSBB Journal
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• v.16 no.4
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• pp.381-388
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• 2001

A program for integrated gene expression profile analysis such as hierarchical clustering, K-means, fuzzy c-means, self-organizing map(SOM), principal component analysis(PCA), and singular value decomposition(SVD) was made for DNA chip data anlysis by using Matlab. It also contained the normalization method of gene expression input data. The integrated data anlysis program could be effectively used in DNA chip data analysis and help researchers to get more comprehensive analysis view on gene expression data of their own.

• The Journal of Korean Medicine
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• v.25 no.1
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• pp.72-84
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• 2004

Objectives : he purpose of this study was to examine the genetic variations and changes of gene expression in the human constitutions. Methods : To analysis variations of individual gene expression, we had selected three groups of volunteers. In each group have a typical constitutional characteristics. By this rime we are analyzed their gene expression patterns by using DNA chip. Results : we can acquire a new information of standard for human constitutions. 1. The 21 genes under express and 3 genes over express in So-Yang constitution 2. The 18 genes under express and 18 genes over express in So-Eum constitution 3. The 16 genes under express and 2 genes over express in Tae-Eum constitution Conclusions : Constitution, QSCCII, Character, Genome, DNA chip.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2004.04a
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• pp.97-100
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• 2004

The identification of the DNA structure as a double-stranded helix consting of two nucleotide chain molecules was a milestone in modern molecular biology. The DNA chip technology is based on reverse hybridization that follows the principle of complementary binding of double-stranded DNA. DNA chip can be described as the deposition of defined nucleic acid sequences, probes, on a solid substrate to form a regular array of elements that are available for hybridization to complementary nucleic acids, targets. DNA chips based on cDNA clons, oligonucleotides and genomic clons have been developed for gene expression studies, genetic variation analysis and genomic changes associated with disease including cancers and genetic diseases. DNA chips for gene expression profiling can be used for functional analysis in human eel Is and animal models, disease-related gene studies, assessment of gene therapy, assessment of genetically modified food, and research for drug discovery. DNA chips for genetic variation detection can be used for the detection of mutations or chromosomal abnormalities in cnacers, drug resistances in cancer cells or pathogenic microbes, histocompatibility analysis for transplantation, individual identification for forensic medicine, and detection and discrimination of pathogenic microbes. The DNA chip will be generalized as a useful tool in clinical diagnostics in near future. Lab-on-a chip and informatics will facilitate the development of a variety of DNA chips for diagnostic purpose.

• Korean Journal of Biological Psychiatry
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• v.8 no.2
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• pp.203-207
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• 2001

The genome sequencing project has generated and will continue to generate enormous amounts of sequence data including 5 eukaryotic and about 60 prokaryotic genomes. Given this ever-increasing amounts of sequence information, new strategies are necessary to efficiently pursue the next phase of the genome project-the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip(or gene microarray) technology was developed to efficiently identify the differential expression pattern of independent biological samples. DNA chip provides a new tool for genome expression analysis that may revolutionize many aspects of biotechnology including new drug discovery and disease diagnostics.

• 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.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.3
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• pp.159-163
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• 2000

The genome sequencing project has generated and will contitute to generate enormous amounts of sequence data. Since the first complete genome sequence of bacterium Haemophilus in fluenzae was published in 1995, the complete genome sequences of 2 eukaryotic and about 22 prokaryotic organisms have detemined. Given this everincreasing amounts of sequence information, new strategies are necessary to efficiently pursue the phase of the geome project- the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip technology was developed to efficienfly identify the differential expression pattern of indepondent biogical samples. DNA chip provides a new tool for genome expreesion analysis that may revolutionize revolutionize many aspects of human kife including mew surg discovery and human disease diagnostics.

• IMMUNE NETWORK
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• v.6 no.3
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• pp.128-137
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• 2006

Background: Apoptosis is a physiologic phenomenon involved in development, elimination of damaged cells, and maintenance of cell homeostasis. Deregulation of apoptosis may cause diseases, such as cancers, immune diseases, and neurodegenerative disorders. The mouse myeloma cell P3-X63-Ag8.653 (v653) is an HGPRT deficient $(HGPRT^-)$ mutant strain. High dependency on de novo transcription and translation of aminopterin induced apoptosis of this cell seems to be an ideal experimental system for searching apoptosis-induced genes. Methods & Results: For searching apoptosis-related genes we carried out GE-array (dot blot), Affymetrix GeneChip analysis, Northern analysis and differential display-PCR techniques. The chip data were analyzed with three different programs. 66 genes were selected through Affymetrix GeneChip analyses. All genes selected were classified into 8 groups according to their known functions. They were Genes of 1) Cell growth/maintenance/death/enzyme, 2) Cell cycle, 3) Chaperone, 4) Cancer/disease-related genes, 5) Mitochondria, 6) Membrane protein/signal transduction, 7) Nuclear protein/nucleic acid binding/transcription binding and 8) Translation factor. Among these groups number of genes were the largest in the genes of cell growth/maintenance/death/enzyme. Expression signals of most of all groups were peaked at 3 hour of apoptosis except genes of Nuclear protein/nucleic acid binding/transcription factor which showed maximum signal at 1 hour. Conclusion: This study showed induction of wide range of proapoptotic factors which accelerate cell death at various stage of cell death. In addition apoptosis studied in this research can be classified as a type 2 which involves cytochrome c and caspase 9 especially in early stages of death. But It also has progressed to type 1 in late stage of the death process.

• BMB Reports
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• v.36 no.4
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• pp.349-353
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• 2003

To explore the application of DNA chip technology for the detection and typing of Human Papillomavirus (HPV), the HPV6, 11, 16 and 18 gene fragments were isolated and printed onto aminosilane-coated glass slides by a PixSys 5500 microarrayer as probes to prepare the HPV gene chips. HPV samples, after being labeled with fluorescent dye by restriction display PCR (RD-PCR) technology, were hybridized with the microarray, which was followed by scanning and analysis. The experimental condition for preparing the HPV gene chips was investigated, and the possibility of HPV genotyping using gene chips was discussed. The technique that was established in this study for preparing HPV gene chips is practical. The results of the present study demonstrated the versatility and inspiring prospect of using this technology to detect and genotype HPV.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.119-122
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• 2000

Biological science is being revolutionized by the availability of much sequence information from many genome project With the advanced technology at hand, main trend in biological research is rapidly changing from a structural DNA analysis to understanding cellular function of the DNA sequences. Combined with mechanics, computer, bioinformatics and other advanced technologies, DNA chip technology provides numerous applications because of its robustness, accuracy, and automation. DNA chip is expected to become an indispensable tool in fields of biology, biotechnology, drug discovery, and other application areas. DNA chip can be used for mutation and polymorphism detection, gene expression monitoring and phenotypic analysis as well. If DNA chip is used for the development of pharmaceutical products, it can considerably reduce the cost and time for the entire process of drug discovery and development, and can also contribute in developing personal drugs.