• 한국생명과학회:학술대회논문집
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• 한국생명과학회 2000년도 제28회 학술심포지엄
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• pp.3-8
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• 2000

The complete genome sequence of a Gram-positive bacterium .Bacillus subtilis has recently been reported and it is now clear that more than 50% of its ORFs have no known function (1). To study the global gene expression in B. subtilis at single gene resolution, we have tested the glass DNA microarrays in a step-wise fashion. As a preliminary experiment, we have created arrays of PCR products for 14 ORF whose transcription patterns have been well established through transcriptional mapping analysis. We measured changes in mRNA transcript levels between early exponential and stationary phase by hybridizing fluorescently labeled cDNA (with Cy3-UTP and Cy5-UTP) onto the array. We then compared the microarray data to confirm that the transcription patterns of these genes are well consistent with the known Northern analysis data. Since the preliminary test has been successful, we scaled up the experiments to ${\sim}$94% of the 4,100 annotated ORFs for the complete genome sequence of B. subtilis. Using this whole genomic microarray, we searched genes that are catabolite-repressive and those that are under the control of ${\sigma}^{Y}$, one of the functionally unknown ECF sigma factors. From these results, we here report that we have established DNA microarray techniques that are applicable for the whole genome of B. subtilis.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제13권1호
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• pp.7-22
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• 2010

목 적: Helicobacter pylori (H. pylori)에 감염된 환자에서 나타나는 결절성 위염은 소아에 특징적인 소견이지만, 지금까지 이에 대한 연구가 이루어지지 못 하였다. 본 연구에서는 H. pylori 감염이 없는 소아 환자의 위 점막의 유전자 발현 양상과 H. pylori에 감염에 의한 결절성 위염이 있는 소아 및 결절성 위염이 없는 소아의 위 점막 유전자 발현 양상을 microarray를 이용하여 비교함으로써 H. pylori 감염 시에 소아의 위 점막에 나타나는 유전자 발현 양상의 변화를 규명하고자 하였다. 방 법: 분당서울대학교 소아청소년과에 내원하여 상 부위장관내시경검사에 의한 위 점막 조직검사를 시행받은 12명의 소아청소년을 대상으로 하였다. 이들을 H. pylori 양성이면서 육안적인 병변이 없는 환아 4명의 HP(+)NG(-)군과, 위 전정부에서 결절성 위염 소견이 관찰된 환아 4명의 HP(+)NG(+)군으로 나누고, 연령 및 성별이 일치하는 H. pylori 음성인 4명의 소아를 대조군인 HP(-)NG(-)군으로 분류하였다. $-70^{\circ}C$에 냉동보관한 위 점막 조직에서 RNA를 추출하여 microarray를 시행하고 분석된 결과에 의거하여 발현 정도에 변화가 있는 유전자를 분석하였다. 결 과: 대상 환자 12명(남자 6명, 여자 6명, 평균 연령 9.8세)의 위 점막 조직에서 cDNA microarray 시행하여 H. pylori 감염의 유무에 따라 유전자 발현 정도를 비교하였을때, H. pylori 감염된 위 점막은 감염되지 않은 소아에 비해 182개의 유전자가 과발현 되었으며, 29개의 유전자가 발현이 저하되었다. H. pylori 감염이 확인 된 8명을 결절성 위염의 유무에 따라 유전자 발현 정도를 비교분석하였을 때, 상부위장관 내시경검사에서 H. pylori 감염과 연관된 결절성 위염을 보인 환자의 위 점막은 결절성 위염이 없는 H. pylori 감염 환아의 위 점막조직에 비해 5개의 유전자가 발현이 증가하였으며 5개의 유전자가 발현이 저하되었다. 결 론: 소아의 위 점막은 H. pylori 감염 여부에 따라 뚜렷한 유전자 발현의 차이를 보이며, 결절성 위염이 동반된 H. pylori 감염 환자의 위 점막은 일부 유전자에서 발현의 차이를 보이는 것을 알 수 있었다. 향후 추가적인 연구를 통해 소아에서 H. pylori 감염에 의한 결절성 위염의 발병 기전을 밝히려는 시도가 필요할 것이다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.357-360
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• 2005

In this paper we consider the well-known semiparametric proportional hazards (PH) models for survival analysis. These models are usually used with few covariates and many observations (subjects). But, for a typical setting of gene expression data from DNA microarray, we need to consider the case where the number of covariates p exceeds the number of samples n. For a given vector of response values which are times to event (death or censored times) and p gene expressions (covariates), we address the issue of how to reduce the dimension by selecting the significant genes. This approach enable us to estimate the survival curve when n < < p. In our approach, rather than fixing the number of selected genes, we will assign a prior distribution to this number. The approach creates additional flexibility by allowing the imposition of constraints, such as bounding the dimension via a prior, which in effect works as a penalty. To implement our methodology, we use a Markov Chain Monte Carlo (MCMC) method. We demonstrate the use of the methodology to diffuse large B-cell lymphoma (DLBCL) complementary DNA(cDNA) data.

• 한국통계학회:학술대회논문집
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• 한국통계학회 2005년도 춘계 학술발표회 논문집
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• pp.17-23
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• 2005

In this paper we consider the well-known semiparametric proportional hazards models for survival analysis. These models are usually used with few covariates and many observations (subjects). But, for a typical setting of gene expression data from DNA microarray, we need to consider the case where the number of covariates p exceeds the number of samples n. For a given vector of response values which are times to event (death or censored times) and p gene expressions(covariates), we address the issue of how to reduce the dimension by selecting the significant genes. This approach enables us to estimate the survival curve when n ${\ll}$p. In our approach, rather than fixing the number of selected genes, we will assign a prior distribution to this number. The approach creates additional flexibility by allowing the imposition of constraints, such as bounding the dimension via a prior, which in effect works as a penalty To implement our methodology, we use a Markov Chain Monte Carlo (MCMC) method. We demonstrate the use of the methodology to diffuse large B-cell lymphoma (DLBCL) complementary DNA (cDNA) data and Breast Carcinomas data.

• 대한약학회:학술대회논문집
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• 대한약학회 2000년도 NEW STRATEGY FOR DRUG DEVELOPMENT IN POST-GENOMIC ERA(대한약학회)
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• pp.55-56
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• 2000

• Asian-Australasian Journal of Animal Sciences
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• 제22권8호
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• pp.1091-1101
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• 2009

In an attempt to understand the biochemical mechanism for the synthesis of the anabolic steroid, 19-nortestosterone, produced by prepubertal boar testes and its physiological role, normalized complementary DNA (cDNA) from boar testes was generated. DNA sequencing of 2,016 randomly selected clones yielded 794,116 base pairs of high quality nucleotide sequence. Computer-assisted assembly of the nucleotide sequence of each clone resulted in 423 contigs and 403 singletons including several genes for steroidogenic enzymes and molecules related to steroid metabolism. Analysis of gene expression pattern by use of the presently-fabricated cDNA microarray identified a number of genes that were differentially expressed during the postnatal development period in boar testes. Two genes of unknown function were identified to be highly expressed in the testis of 2-weeks-old neonatal boar. In addition, the sequencing of open reading frames of these genes revealed their homology with human alpha hemoglobin and Homo sapiens hypothetical LOC643669, transcript variant 1. Moreover, the transcripts of these genes were also detected in porcine muscle and adipocytes, in addition to Leydig cells of pigs.

• Journal of Periodontal and Implant Science
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• 제36권3호
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• pp.613-625
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• 2006

Periodontal ligament(PDL) cells and human gingival fibroblasts(HGFs) play important roles in development, regeneration, normal function, and pathologic alteration. PDL cells and HGFs have the similarity related with general characteristics of fibroblast such as spindle shaped morphology, the presence of vimentin intermediate filament and the synthesis of interstitial collagens and fibronectin. There were many studies about the differences between PDL cells and HGFs, but they were not about whole gene level. In this study, we tried to explain the differences of gene expression profiles between PDL cells and HGFs, and the differences among three individuals by screening gene expression patterns of PDL cells and HGFs, using cDNA microarray. Although there were some variants among three experiments, a set of genes were consistentely and differentially expressed in one cell type. Among 3,063 genes, 49 genes were more highly expressed in PDL cells and 12 genes were more highly expressed in HGFs. The genes related with cell structure and motility were expressed more highly in PDL cells. These are cofilin 1, proteoglycan 1 secretory granule, collagen type I(${\alpha}$ 1), adducin gamma subunit, collagen type III(${\alpha}$ 1), fibronectin, lumican(keratan sulfate proteoglycan), and ${\alpha}$ -smooth muscle actin. Tissue inhibitor of metalloproteinase known as the enzyme controlling extracellular matrix with matrix metalloproteinase is more highly expressed in PDL cells, osteoprotegerin known as osteoclastogenesis inhibitory factor is more highly expressed in HGFs. We performed northern blot to verify cDNA microarray results on selected genes such as tissue inhibitor of metalloproteinase, fibronectin, osteoprogeterin. The result of northern blot analysis showed that each cell expressed the genes in similar pattern with cDNA microarray result. This result indicates that cDNA microarray is a reliable method in screening of gene expression profiles.

• Asian Pacific Journal of Cancer Prevention
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• 제16권8호
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• pp.3543-3549
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• 2015

Background: Bladder cancer is one of the most common cancers worldwide. Gene expression profiling using microarray technologies improves the understanding of cancer biology. The aim of this study was to determine the gene expression profile in Egyptian bladder cancer patients. Materials and Methods: Samples from 29 human bladder cancers and adjacent non-neoplastic tissues were analyzed by cDNA microarray, with hierarchical clustering and multidimensional analysis. Results: Five hundred and sixteen genes were differentially expressed of which SOS1, HDAC2, PLXNC1, GTSE1, ULK2, IRS2, ABCA12, TOP3A, HES1, and SRP68 genes were involved in 33 different pathways. The most frequently detected genes were: SOS1 in 20 different pathways; HDAC2 in 5 different pathways; IRS2 in 3 different pathways. There were 388 down-regulated genes. PLCB2 was involved in 11 different pathways, MDM2 in 9 pathways, FZD4 in 5 pathways, p15 and FGF12 in 4 pathways, POLE2 in 3 pathways, and MCM4 and POLR2E in 2 pathways. Thirty genes showed significant differences between transitional cell cancer (TCC) and squamous cell cancer (SCC) samples. Unsupervised cluster analysis of DNA microarray data revealed a clear distinction between low and high grade tumors. In addition 26 genes showed significant differences between low and high tumor stages, including fragile histidine triad, Ras and sialyltransferase 8 (alpha) and 16 showed significant differences between low and high tumor grades, like methionine adenosyl transferase II, beta. Conclusions: The present study identified some genes, that can be used as molecular biomarkers or target genes in Egyptian bladder cancer patients.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.51-56
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• 2005

There are many sources of systematic variations in cDNA microarray experiments which affect the measured gene expression levels like differences in labeling efficiency between the two fluorescent dyes. Print-tip lowess normalization is used in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. However, print-tip lowess normalization performs poorly in situation where error variability for each gene is heterogeneous over intensity ranges. We proposed the new print-tip normalization methods based on support vector machine regression(SVMR) and support vector machine quantile regression(SVMQR). SVMQR was derived by employing the basic principle of support vector machine (SVM) for the estimation of the linear and nonlinear quantile regressions. We applied our proposed methods to previous cDNA micro array data of apolipoprotein-AI-knockout (apoAI-KO) mice, diet-induced obese mice, and genistein-fed obese mice. From our statistical analysis, we found that the proposed methods perform better than the existing print-tip lowess normalization method.

• Molecular & Cellular Toxicology
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• 제2권2호
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• pp.141-149
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• 2006

Tamoxifen (TAM), a non-steroidal anti estrogen anticancer drug and chemopreventive agent for breast cancer, have caused cholestasis in liver. The potent hepatocarcinogenicity of this drug has been reported. Methotrexate (MTX) is dihydrofolate reductase inhibitor which interfaces with the synthesis for urine nucleotide and dTMP. And it may cause atrophy, necrosis and steatosis in liver. These two anticancer drug have well-known hepatotoxicity. So, in this study we compare the gene expression pattern of antitumor agent TAM and MTX, using the cDNA microarray. We have used 4.8 K cDNA microarray to identify hepatotoxicity-related genes in 5-week-old male Sprague-Dawley (SD) rats. Confirm the pattern of gene expression, we have used Real time PCR for targeted gene. In the case of MTX, Protease related gene (Ctse, Ctsk) and Protein kinase (Pctk 1) have shown specific expression pattern. And in the case of TAM, apoptosis related gene (Pdcd 8) and signal transduction related gene (kdr) have significantly up regulated during treatment time. Gene related with growth factor, lipid synthesis, chemokins were significantly changed. From the result of this study, the information about influence of TAM and MTX to hepatoxicity will provide.