• Journal of Pharmacopuncture
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• v.8 no.3
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• pp.57-69
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• 2005

Objectives : Neurological disorders have been one of main therapeutic targets of acupuncture. The present study investigated the protective effects of Gwakhyangjeonggisan herbal acupuncture solution (GHAS). Methods : We performed 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay in glioblastoma cells, and did microarray analysis with cells exposed to reactive oxigen species (ROS) of hydrogen peroxide by 8.0 k Human cDNA, with cut-off level of 2-fold changes in gene expression. Results : MTT assay showed protective effect of GHAS on the glioblastoma cells exposed to hydrogen peroxide. When glioblastoma cells were exposed to hydrogen peroxide, 24 genes were downregulated. When the cells were pretreated with GHAS before exposure to hydrogen peroxide, 46 genes were downregulated. Many of the genes downregulated by hydrogen peroxide stimulation were decreased in the amount of downregulation or reversed to upregulation. Conclusions : The gene expression changes observed in the present study are supposed to be related to the protective molecular mechanism of GHAS in the glioblastoma cells exposed to ROS stress.

• Journal of Acupuncture Research
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• v.22 no.6
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• pp.111-123
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• 2005

Objectives : Neurological disorders have been one of main therapeutic targets of acupuncture. The present study investigated the protective effects of Gwakhyangjeonggisan herbal acupuncture solution (GHAS). Methods : We performed 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay in glioblastoma cells, and did microarray analysis with cells exposed to reactive oxigen species (ROS) of hydrogen peroxide by 8.0 k Human cDNA, with cut-off level of 2-fold changes in gene expression. Results : MTT assay showed protective effect of GHAS on the glioblastoma cells exposed to hydrogen peroxide. When glioblastoma cells were exposed to hydrogen peroxide, 16 genes were upregulated. When the cells were pretreated with GHAS before exposure to hydrogen peroxide, 22 genes were upregulated. Most of the genes upregulated by hydrogen peroxide stimulation were reversed to downregulation by GHAS. Conclusion : The gene expression changes observed in the present study are supposed to be related to the protective molecular mechanism of GHAS in the glioblastoma cells exposed to ROS stress.

• Molecular & Cellular Toxicology
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• v.5 no.1
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• pp.1-6
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• 2009

Microglial cells constitute the first line of defense against infection and injury in the brain. This study was conducted to evaluate the protective mechanisms of Agrimonia pilosa (AP) on LPS-induced activation of BV-2 microglial cells. The effects of AP on gene expression profiles in activated BV-2 microglial cells were evaluated using microarray analysis. BV-2 microglial cells were cultured in a 100 mm dish ($1{\times}10^7/mL$) for 24 hr and then pretreated with 1 g/mL AP or left untreated for 30 min. Next, 1 g/mL LPS was added to the samples and the cells were reincubated at $37^{\circ}C$ for 30 min, 3 hr and 6 hr. The gene expression profiles of the BV-2 microglial cells varied depending on the AP. The microarray analysis revealed that MAPK signaling pathway-related genes were down-regulated and IL10 gene was up-regulated in AP-treated BV-2 microglial cells. AP can affect the inflammatory response and MAPK pathway in BV-2 microglial cells.

• Korean Journal of Environmental Biology
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• v.22 no.3
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• pp.472-477
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• 2004

To study the radiation related gene expression in mutants of Bacillus lentimorbus WJ5 induced by gamm radiation, the simultaneous gene expression was analyzed by DNA micro array. We constructed DNA chips including two thousand randomly digested genome spots of B. lentimorbus WJ5 and compared its quantitative aspect with seven mutants induced by gamma radiation $(^{60}/Co)$. From the cluster analysis of gene expression pattern, totally 408 genes were expressed and 27 genes were significantly upregulated by the gamma radiation in all mutants. Especially, genes involved in repair (mutL, mutM), energy metabolism (acsA, sdhB, pgk, yhjB, citB), protease (npr), and reduction response to oxidative stress (HMM) were simultaneously upregulated. It seems that the induction of the direct and/or indirect repair related genes in mutants induced by gamma radiation could be remarkably different from the adaptive responses against acute exposure to radiation.

• Preventive Nutrition and Food Science
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• v.8 no.4
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• pp.390-394
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• 2003

In the post-genome period, the technique for identifying gene expression has been progressed to high throughput screening. In the field of molecular nutrition, the use of screening techniques to clarify molecular function of specific nutrients would be very advantageous. In this study, we have evaluated Zn-regulated gene expression in Zn-deficient, homocystein-treated EA.hy926 cells, using cDNA microarray, which can be used to screen the expression of many genes simultaneously. The information obtained can be used for preliminary assessment of molecular and signaling events modulated by Zn under pro-atherogenic conditions. EA.hy926 cells derived from human umbilical vein endothelial cells were cultured in Zn-adequate (control, 15 $\mu$M Zn) or Zn-deficient (experimental, 0 $\mu$M Zn) Dulbecco's MEM media under high homocysteine level (100 $\mu$M) for 3 days of post-confluency. Cells were harvested and RNA was extracted. Total RNA was reverse-transcribed and the synthesized cDNA was labeled with Cy3 or Cy5. Fluorescent labeled cDNA probe was applied to microarray slides for hybridization, and the slide was then scanned using a fluorescence scanner. The expression of seven genes was found to be significantly decreased, and one significantly increased, in response to treatment of EA.hy926 cells with Zn-deficient medium, compared with Zn-supplemented medium. The upregulated genes were oncogenes and tumor suppressor genes, cell cycle-related genes and transporter genes. The down-regulated gene was RelB, a component of the NF-kappaB complex of transcription factors. The results of this study imply the effectiveness of cDNA microarray for expression profiling of a singly nutrient deficiency, namely Zn. Furthur study, using tailored-cDNA array and vascular endothelial cell lines, would be beneficial to clarify the molecular function of Zn in atherosclerosis, more in detail.

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.248-255
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• 2005

To understand the response of cancer cells to anticancer drugs at the gene expression level, we examined the gene expression changes in response to five anticancer drugs, 5-fluorouracil, cytarabine, cisplatin, paclitaxel, and cytochalasin D in NCI-H460 human lung cancer cells. Of the five drugs, 5-fluorouracil had the most distinctive gene expression signature. By clustering genes whose expression changed significantly, we identified three clusters with unique gene expression patterns. The first cluster reflected the up-regulation of gene expression by cisplatin, and included genes involved in cell death and DNA repair. The second cluster pointed to a general reduction of gene expression by most of the anticancer drugs tested. A number of genes in this cluster are involved in signal transduction that is important for communication between cells and reception of extracellular signals. The last cluster represented reduced gene expression in response to 5-fluorouracil, the genes involved being implicated in DNA metabolism, the cell cycle, and RNA processing. Since the gene expression signature of 5-fluorouracil was unique, we investigated it in more detail. Significance analysis of microarray data (SAM) identified 808 genes whose expression was significantly altered by 5-fluorouracil. Among the up-regulated genes, those affecting apoptosis were the most noteworthy. The down-regulated genes were mainly associated with transcription-and translation-related processes which are known targets of 5-fluorouracil. These results suggest that the gene expression signature of an anticancer drug is closely related to its physiological action and the response of caner cells.

• Communications for Statistical Applications and Methods
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• v.16 no.3
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• pp.397-408
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• 2009

The development of microarray technology makes possible to analyse many thousands of genes simultaneously. While it is important to test each gene whether it shows changes in expression associated with a phenotype, human diseases are thought to occur through the interactions of multiple genes within a same functional cafe-gory. Recent research interests aims to directly test the behavior of sets of functionally related genes, instead of focusing on single genes. Gene set enrichment analysis(GSEA), significance analysis of microarray to gene-set analysis(SAM-GS) and parametric analysis of gene set enrichment(PAGE) have been applied widely as a tool for gene-set analyses. We describe their problems and propose an alternative method using a parametric analysis by adopting normal score transformation of gene expression values. Performance of the newly derived method is compared with previous methods on three real microarray datasets.

• Journal of KIISE:Computer Systems and Theory
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• v.30 no.10
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• pp.544-555
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• 2003

Since the result data from DNA microarray experiments contain a lot of gene expression information, adequate analysis methods are required. Hierarchical clustering is widely used for analysis of gene expression profiles. In this paper, we study leaf-ordering, which is a post-processing for the dendrograms output by hierarchical clusterings to improve the efficiency of DNA microarray data analysis. At first, we analyze existing leaf-ordering algorithms and then present new approaches for leaf-ordering. And we introduce a software HCLO(Hierarchical Clustering ＆ Leaf-Ordering Tool) that is our implementation of hierarchical clustering, some of existing leaf-ordering algorithms and those presented in this paper.

• Proceedings of the Korean Society of Embryo Transfer Conference
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• 2005.10a
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• pp.108-108
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• 2005

• Journal of Acupuncture Research
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• v.23 no.4
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• pp.135-148
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• 2006

Objectives : Juglandis Semen herbal acupuncture solution(JSS) has a broad array of clinical applications in oriental medicine, including treatment of chronic musculoskeletal diseases such as arthritis. This study was performed to investigate the global gene expression profiles using microarray assay in RAW 264.7 cell line treated with JSS and to advance our understanding of the pharmacologic effect of Jss. Methods : Change of the gene expression profile in RAW cell line following treatment with JSS alone, with lipopolysaccharide(LPS) alone, or with LPS plus JSS was investigated with a cut-off level of 2 fold change in the expression. Results : Of the 8170 genes profiled in this study, 95 were upragulated and 42 downregulated following JSS treatment, 51 were upragulated and 21 downregulated following LPS treatment, and 88 were upregulated and 69 downregulated following costimulation of JSS and LPS. Conclusion : JSS treatment induced upregulation of some genes including IL-10 with its possible implication in an antiinflammatory action of JSS. However, further research on expression profile changes induced by JSS treatment is expected.