• Communications for Statistical Applications and Methods
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• 제12권2호
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• pp.335-348
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• 2005

The rapid development of microarray technologies enabled the monitoring of expression levels of thousands of genes simultaneously. Recently, the time course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. For the data, biologists are attempting to group genes based on the temporal pattern of their expression levels. We apply the consensus clustering algorithm to a time course gene expression data in order to infer statistically meaningful information from the measurements. We evaluate each of consensus clustering and existing clustering methods with various validation measures. In this paper, we consider hierarchical clustering and Diana of existing methods, and consensus clustering with hierarchical clustering, Diana and mixed hierachical and Diana methods and evaluate their performances on a real micro array data set and two simulated data sets.

• BMB Reports
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• 제30권1호
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• pp.41-45
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• 1997

The present study was performed to analyze the molecular mechanism which dictates the transcription regulation of the $O^6$-methylguanine-DNA methyltransferase (MGMT) gene in Saccharomyces cerevisiae. Previously we identified one possible upstream repressing sequence (URS) in MGMT promoter by promoter deletion and competition analysis. In this paper we report another regulatory element (UAS: upstream activating sequence. -213 to -136) which affects the transcription activity of MGMT promoter. Gel mobility shift assay and Southwestern blot analysis using UAS probe showed several specific proteins which were able to bind to this sequence.

• 한국생명과학회:학술대회논문집
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• 한국생명과학회 2006년도 제47회 학술심포지움 및 추계국제학술대회
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• pp.109.2-109.2
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• 2006

• 한국식물병리학회지
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• 제11권1호
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• pp.66-72
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• 1995

The coat protein (CP) gene of cucumber mosaic virus-As (CMV-As) strain was engineered for expression in the plant by using the cauliflower mosaic virus 35S transcript regulatory sequences. The CP gene was cloned into an Agrobacterium-derived binary vector. A chimeric gene was constructed by the cDNA of CMV-As CP and plant expression vector pBI121. The clone, pCMAS66, was first introduced into the phagemid vector pSPORT1 for situating sense orientation for translation and making restriction sites in order to re-introduce plant expression vector, pHI121. The resulting subclone pCASCP02 and plant expression vector pBI121 were treated with BamHI-SacI for excising the target gene and removing GUS gene, respectively. After Agrobacterium transformation by freeze-thaw technique, the clone, pCMASCP121-123 which contains sense orientation of the target gene, was selected and confirmed by restriction endonuclease analysis. The CMV-As CP gene was introduced into A. tumefaciens. The results on tobacco plant transformation with the vector system revealed that the system could be successfully introduced and showed high frequency of selection to putative transformations.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.39-49
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• 2004

When there is a lack of detailed kinetic information, dFBA(dynamic flux balance analysis) has correctly predicted cellular behavior under given environmental conditions with FBA and different ial equations. However, until now, dFBA has centered on substrate concentration, cell growth, and gene on/off, but a detailed hierarchical structure of a regulatory network has not been taken into account. For this reason, the dFBA has limited the represen tation of interactions between specific regulatory proteins and genes and the whole transcriptional regulation mechanism with environmental change. Moreover, to calculate optimal metabolic flux distribution which maximizes the growth flux and predict the b ehavior of cell system, linear programming package(LINDO) and spreadsheet package(EXCEL) have been used simultaneously. thses two software package have limited in the visual representation of simulation results and it can be difficult for a user to look at the effects of changing inputs to the models. Here, we descirbes the construction of hierarchical regulatory network with defined symbolsand the development of an integrated system that can predict the total control mechanism of regulatory elements (opero ns, genes, effectors, etc.), substrate concentration, growth rate, and optimal flux distribution with time. All programming procedures were accoplished in a visual programming environment (LabVIEW).

• Genomics & Informatics
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• 제9권3호
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• pp.127-133
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• 2011

The Epstein-Barr virus-transformed lymphoblastoid cell line (LCL) is one of the major genomic resources for human genetics and immunological studies. Use of LCLs is currently extended to pharmacogenetic studies to investigate variations in human gene expression as well as drug responses between individuals. We evaluated four common internal controls for gene expression analysis of selected hematopoietic transcriptional regulatory genes between B cells and LCLs. In this study, the expression pattern analyses showed that TBP (TATA box-binding protein) is a suitable internal control for normalization, whereas GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is not a good internal control for gene expression analyses of hematopoiesis-related genes between B cells and LCLs at different subculture passages. Using the TBP normalizer, we found significant gene expression changes in selected hematopoietic transcriptional regulatory genes (downregulation of RUNX1, RUNX3, CBFB, TLE1, and NOTCH2 ; upregulation of MSC and PLAGL2) between B cells and LCLs at different passage numbers. These results suggest that these hematopoietic transcriptional regulatory genes are potential cellular targets of EBV infection, contributing to EBV-mediated B-cell transformation and LCL immortalization.

• 한국가금학회지
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• 제50권4호
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• pp.261-266
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• 2023

가축의 골격근은 동물성 단백질 식품으로서 중요한 역할을 하며, 가금육의 소비는 전세계적으로 꾸준히 증가하고 있다. 근육의 형성과 발달에는 근형성조절인자를 포함한 많은 유전자들이 관여하며, 발달 단계에 따라 유전자 발현의 정확한 조절이 필요하다. 본 연구에서는 근육에서 특이적으로 발현하는 유전자를 선발하고, 해당 유전자의 프로모터를 클로닝하고 기능을 분석하였다. 동물의 조직별 유전자 발현을 분석한 결과, 다수의 유전자들이 골격근 특이적인 발현양상을 보였는데, 특히 TNNT3와 TNNC2, MYF6 유전자들은 가금에서도 유사한 양상을 나타냈다. TNNT3, TNNC2, MYF6 유전자의 프로모터 부위를 중합효소연쇄반응을 통해 각각 1.2 kb, 1.03 kb, 1.43 kb씩 증폭하여, 녹색형광단백질 유전자를 포함한 벡터의 앞부분에 삽입하였다. 염기서열 분석 결과, 세 프로모터는 기존에 밝혀진 유전체 서열과 거의 일치함을 확인하였다. QM7 메추리 근육세포주에서 각각의 프로모터를 포함한 벡터를 도입한 결과, 세 프로모터 모두녹색형광단백질을 성공적으로 발현시켰다. 녹색 형광의 밝기는 대조군으로 사용한 CMV-IE 프로모터와 비교 시, 약 7배 정도 어두웠다. 클로닝한 프로모터들에는 230개 이상의 전사인자들이 결합할 수 있을 것으로 예측되었으며, 특히 MYF5나 MYOD, MYOG와 같은 근형성조절인자를 포함한 근육에서 발현하는 다양한 전사인자들이 결합할 수 있을 것으로 예측되었다. 이 프로모터들은 가금의 근육세포에서 유전자 발현을 유도하는 연구에 활용이 가능할 것이며, 추후연구를 통해 프로모터 부위별 발현 조절 기능 연구가 필요할 것으로 사료된다.

• BMB Reports
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• 제32권5호
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• pp.456-460
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• 1999

The promoter of the HSV-1 VP16 gene contains binding sites for the cellular transcription factors such as USF, CTF, and Sp1, each of which affects basal level expression of the VP16 gene. Transcription of the VP16 gene was induced by viral immediate-early proteins, ICP0 and ICP4, in a synergistic manner but repressed by ICP22. To gain further insight into the role of ICP0 in the expression of the VP16 gene during virus infection, several mutants with deletions in each of their transcriptional regulatory elements were generated. According to transient gene expression assays of these mutants using the CAT gene as a reporter, the USF and CTF binding sites were necessary for efficient induction of the promoter in the presence of transfected ICP0 or during virus infection, whereas the Sp1 binding site had little effect on ICP0-mediated VP16 expression. These results indicate that the immediate early proteins of HSV-1 regulate expression of the VP16 gene during virus infection by modulating the activities of cellular transcription factors such as USF and CTF.

• Journal of Microbiology and Biotechnology
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• 제20권11호
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• pp.1484-1490
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• 2010

In the Streptomyces hygroscopicus JCM4427 geldanamycin biosynthetic gene cluster, five putative regulatory genes were identified by protein homology searching. Among those genes, gel14, gel17, and gel19 are located downstream of polyketide synthase genes. Gel14 and Gel17 are members of the LAL family of transcriptional regulators, including an ATP/GTP-binding domain at the N-terminus and a DNA-binding helix-turn-helix domain at the C-terminus. Gel19 is a member of the TetR family of transcriptional regulators, which generally act to repress transcription. To verify the biological significance of the putative regulators in geldanamycin production, they were individually characterized by gene disruption, genetic complementation, and transcriptional analyses. All three genes were confirmed as positive regulators of geldanamycin production. Specifically, Gel17 and Gel19 are required for gel14 as well as gelA gene expression.

• Toxicological Research
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• 제31권1호
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• pp.1-9
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• 2015

Environmental toxicants such as toxic metals can alter epigenetic regulatory features such as DNA methylation, histone modification, and non-coding RNA expression. Heavy metals influence gene expression by epigenetic mechanisms and by directly binding to various metal response elements in the target gene promoters. Given the role of epigenetic alterations in regulating genes, there is potential for the integration of toxic metal-induced epigenetic alterations as informative factors in the risk assessment process. Here, we focus on recent advances in understanding epigenetic changes, gene expression, and biological effects induced by toxic metals.