• 한국통계학회:학술대회논문집
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• 한국통계학회 2003년도 춘계 학술발표회 논문집
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• pp.299-304
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• 2003

생물학자들은 시간 패턴에 따라 발현 수준이 변화하는 유전자의 군집화를 시도하고 있다. 지금까지는 군집 방법의 비교 연구가 주로 진행되어 왔으나, 군집화 이전의 유전선택 방법에 따라 군집화 결과가 달라지기 때문에 유전자 선택 단계도 같이 고려되어야 한다. 따라서 본 연구에서는 Time Control Microarray 자료를 가지고 군집 분석을 하는데 있어서 유전자 선택, 군집분석 방법의 선택, Validation 방법의 선택 등 3가지 요인별로 보다 폭 넓은 비교 연구를 하였다.

• 응용통계연구
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• 제21권1호
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• pp.65-80
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• 2008

소규모 경시적 마이크로어레이 실험이란 시점의 개수가 적은 경시적 마이크로어레이 실험으로서 현재까지 보고된 경시적 마이크로어레이 실험의 약 80%를 차지한다. 최근 들어 소규모 경시적 마이크로어레이 실험을 대상으로 하는 통계적 분석 방법이 몇 가지 제안되었다. 최근에 제안된 세 가지 방법들을 실제 소규모 경시적 마이크로어레이 실험자료에 적용하여 분석하고 모의실험 자료를 생성하여 각 방법들의 검정력과 위양성율을 비교해 보았다. 그 결과 낮은 위양성율을 보이는 STEM방법이 다른 방법에 비해서 우위에 있음이 드러났다.

• Molecular & Cellular Toxicology
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• 제1권2호
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• pp.92-98
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• 2005

DNA microarray analysis of gene expression in toxicogenomics typically requires relatively large amounts of total RNA. This limits the use of DNA microarray when the sample available is small. To confront this limitation, different methods of linear RNA amplification that generate antisense RNA (aRNA) have been optimized for microarray use. The target preparation strategy using amplified RNA in DNA microarray protocol can be divided into direct-incorporation labeling which resulted in cDNA targets (Cy-dye labeled cDNA from aRNA) and indirect-labeling which resulted in cRNA targets (i.e. Cy-dye labeled aRNA), respectively. However, despite the common use of amplified targets (cDNA or cRNA) from aRNAs, no systemic assessment for the use of amplified targets and bias in terms of hybridization performance has been reported. In this investigation, we have compared the hybridization performance of cRNA targets with cDNA targets from aRNA on a 10 K cDNA microarrays. Under optimized hybridization conditions, we found that 43% of outliers from cDNA technique and 86% from the outlier genes were reproducibly detected by both targets hybridization onto cDNA microarray. This suggests that the cRNA labeling method may have a reduced capacity for detecting the differential gene expression when compared to the cDNA target preparation. However, further validation of this discordant result should be pursued to determine which techniques possesses better accuracy in identifying truly differential genes.

• Communications for Statistical Applications and Methods
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• 제13권3호
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• pp.567-576
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• 2006

In this paper, we applied the multiblock dimension reduction methods to the classification of tumor based on microarray gene expressions data. This procedure involves clustering selected genes, multiblock dimension reduction and classification using linear discrimination analysis and quadratic discrimination analysis.

• 한국한의학연구원논문집
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• 제14권1호
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• pp.145-160
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• 2008

Nelumbinis Semen(NS) has been used in traditional medicine to treat diseases such as depression and diarrhea. In inflammatory responses, microglia produces molecules which are known to play roles in the central nervous system. And we previously studied NS inhibited nitric oxide synthase and secretion of tumor necrosis factor alpha. To explore the global gene expression profiles in BV-2 microglial cell line treated with NS, microarray analysis was performed. The cells were treated with LPS or NS plus LPS for 30min, Ih, 3h, and 6h, respectively. Of 45,101 known genes, with cutoff value of 3-fold change in the expression, 340, 644, 280 and 219 genes were upregulated and 503, 570, 694 and 484 were downregulated in NS treated cells at each time point. The results of the present study shows that treatment of NS reversed the LPS-induced upregulation of such genes as Ecoxsackievirus and adenovirus receptor(CAR), pellino 1, and S100P binding protein. It is thought that microarrays will play an ever-growing role in the advance of our understanding of the pharmacologic actions NS.

• 응용통계연구
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• 제18권2호
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• pp.355-369
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• 2005

마이크로어레이 실험에서는 유전자의 기능과 상호작용의 이해를 돕기 위한 방안으로 유전자발현자료의 시각화방법이 많이 사용되고 있다. 행렬도는 유전자와 샘플들을 동시에 그려볼 수 있어서, 유전자 또는 샘플의 군집이나 유전자-샘플간 연관작용을 알아보는데 더욱 유용하게 쓰일 수 있다. 본고에서는 마이크로어레이실험에서 행렬도를 이용하여 유전자의 군집 및 연관성을 알아보는 방법을 소개하고, 추가점기법을 이용하여 새로운 샘플을 분류하는 방법을 제안하였다. Golub et al.(1999)의 백혈병 데이터와 Alizadeh et al. (2000)의 림프구데이터, Ross et al.(2000)의 NCI60 종양조직데이터를 이용하여 유용성을 살펴보았으며, 계층적 군집분석 및 k-평균 군집분석 등 다른 기법을 이용한 결과와 비교하고 이러한 기법을 행렬도와 연계하는 방안을 살펴보았다.

• Asian-Australasian Journal of Animal Sciences
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• 제16권12호
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• pp.1837-1841
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• 2003

In an attempt to isolate novel molecules that may play a regulatory role in adipocyte differentiation, we devised an experimental strategy to identify adipose tissue-specific genes by modifying cDNA microarray technique. We used genefilter membranes containing approximately 15,000 rat non-redundant EST clones of which 4,000 EST were representative clones of known genes and 11,000 ESTs were uncharacterized clones. A series of hybridization of genefilter membranes with cDNA probes prepared from various rat tissues and nucleic acids sequence analysis allowed us to identify two adipose-tissue specific genes, adipocyte-specific secretory factor (ADSF) and H-rev107. Verification of tissue-specific expression patterns of these two genes by Northern blot analysis showed that ADSF mRNA is exclusive expressed in adipose tissue and the H-rev107 mRNA is predominantly expressed in adipose tissue. Further analysis of gene expression of ADSF and H-rev107 during 3T3-L1 adipocyte differentiation revealed that the ADSF and H-rev107 gene expression patterns are closely associated with the adipocyte differentiation program, indicating their possible role in the regulation of adipose tissue development. Overall, we demonstrated an application of modified cDNA microarray technique in molecular cloning, resulting in identification of two novel adipose tissue-specific genes. This technique will also be used as a useful tool in identifying novel genes expressed in a tissue-specific manner.

• Biomolecules & Therapeutics
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• 제15권3호
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• pp.192-198
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• 2007

Emodin (1,3,8-trihydroxy-6-methylanthraquinone) is a major constituent of rhubarb. Although it has been claimed to have a wild spectrum of therapeutic value, its side effects, especially in human kidney cells have not been well characterized. In this study, we have carried out in vitro genetic toxicity test of emodin and microarray analysis of differentially expressed genes in response to emodin. The result of Ames test showed mutations with emodin treatment in base substitution strain TA1535 both with and without exogenous metabolic activation. Likewise, emodin showed mutations in frame shift TA98 both with and without exogenous metabolic activation. The result of COMET assay in L5178Y cells with emodin treatment showed DNA damage both with and without exogenous metabolic activation. Emodin did not increase micronuclei in CHO cells both with and without exogenous metabolic activation. 150 Genes were selected as differentially expressed genes in response to emodin by microarray analysis and these genes would be candidate biomarkers of genetic toxic action of emodin.

• Biomolecules & Therapeutics
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• 제15권3호
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• pp.199-204
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• 2007

Carbamates have excellent insecticidal activities against a broad spectrum of insects. They possess knocking-down, fast-killing, and systemic effects, however, they are toxic to mammals. In this study, we have carried out in vitro genetic toxicity test of methylcarbamate and microarray analysis of differentially expressed genes in response to methylcarbamate. Methylcarbamate did not show mutations in base substitution strain TA1535 both with and without exogenous metabolic activation. Methylcarbamate did not show mutations in frame shift TA98 both with and without exogenous metabolic activation. Methylcarbamate showed DNA damage based on single cell gel/comet assay in L5178Y cells both with and without exogenous metabolic activation. Methylcarbamate did not increase micronuclei in CHO cells both with and without exogenous metabolic activation. Microarray analysis of gene expression profiles in L5178Y cells in response to methylcarbamate selected differentially expressed 132 genes that could be candidate biomarkers of genetic toxic action of methylcarbamate.

• 한국정보과학회논문지:시스템및이론
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• 제30권10호
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• pp.544-555
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• 2003

DNA 마이크로어레이 실험으로 나오는 데이타는 아주 많은 양의 유전자 발현 정보를 담고 있기 때문에 적절한 분석 방법이 필요하다. 대표적인 분석 방법은 계층적 클러스터링(hierarchical clustering) 방법이다. 본 논문에서는 계층적 클러스터링의 결과로 나오게 되는 덴드로그램(dendrogram)에 대해서 후처리(post-Processing)를 시행함으로써 DNA 마이크로어레이 데이타 분석을 더 용이하게 해주는 리프오더링(leaf-ordering)에 대해서 연구하였다. 먼저, 기존의 리프오더링 알고리즘들을 분석하였고, 리프오더링 알고리즘의 새로운 접근 방식을 제안하였다. 또한 이에 대한 성능을 실험하고 분석하기 위해서 계층적 클러스터링과 몇 가지 리프오더링 알고리즘들, 그리고 제안된 접근 방식을 직접 구현한 HCLO (Hierarchical Clustering & Leaf-Ordering Tool)에 대해서 소개하였다.