• Molecules and Cells
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• v.20 no.1
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• pp.57-68
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• 2005

Murine erythroleukemia (MEL) cells are widely used to study erythroid differentiation thanks to their ability to terminally differentiate in vitro in response to chemical induction. At the molecular level, not much is known of their terminal differentiation apart from activation of adult-type globin gene expression. We examined changes in gene expression during the terminal differentiation of these cells using microarray-based technology. We identified 180 genes whose expression changed significantly during differentiation. The microarray data were analyzed by hierarchical and k-means clustering and confirmed by semi-quantitative RT-PCR. We identified several genes including H1f0, Bnip3, Mgl2, ST7L, and Cbll1 that could be useful markers for erythropoiesis. These genetic markers should be a valuable resource both as potential regulators in functional studies of erythroid differentiation, and as straightforward cell type markers.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.5
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• pp.444-450
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• 2005

Epidermal growth factor (EGF) activates many intracellular effector molecules, which subsequently influence the expression levels of many genes involved in cell growth, apoptosis and signal transduction, etc. In this study, the early response of gene expressions due to EGF treatment was monitored using oligonucleotide DNA microarrays in rat schwannoma cell lines. An immunoblotting experiment showed the successful activation of EGF receptors and an effector protein, STAT5, due to EGF treatment. The microarray study showed that 35 genes were significantly induced and 2 were repressed within 60 min after the treatment. The list of induced genes included early growth response 1, suppressor of cytokine signaling 3, c-fos, interferon regulatory factor 1 and early growth response 2, etc. According to the microarray data, six of these were induced by more than 10-fold, and showed at least two different induction patterns, indicating complicated regulatory mechanisms in the EGF signal transduction.

• Environmental Analysis Health and Toxicology
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• v.20 no.2 s.49
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• pp.187-194
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• 2005

Octachlorostyrene (OCS) is a primarily concerning chemical in many countries because of its persistent and bioaccumulative properties in the environment. OCS is not commercially manufactured or used but it may be produced during incineration or chemical synthetic processes involving chlorinated compounds. There are several reports that OCS was found in the waters, sediments, fish, mussels, and also in human tissues. However, systematic studies on the OCS toxicities are scarce in literature. In this study, we tried to get the gene expression data using medaka DNA chip to identify biomarkers of OCS exposure. Medaka (Oryzias latipes.) was exposed to OCS 1 ppm for 2 days and 10 days, respectively. Total RNA was extracted and purified by guanidine thiocyanate method and the Cy3- and Cy5-labelled cDNAs produced by reverse trancription of the RNA were hybridized to medaka microarray. As results, eighty five genes were found to be down-or up regulated by OCS. Some of the genes were listed and confirmed by real-time PCR.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.124-130
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• 2004

Microarray expression datasets are incessantly cumulated with the aid of recent technological advances. One of the first steps for analyzing these data under various experimental conditions is determining differentially expressed genes (DEGs) in each condition. Reasonable choices of thresholds for determining differentially expressed genes are used for the next -step-analysis with suitable statistical significances. We present a model for identifying DEGs using pathway information based on the global connectivity structure. Pathway information can be regarded as a collection of biological knowledge, thus we are tying to determine the optimal threshold so that the consequential connectivity structure can be the most compatible with the existing pathway information. The significant feature of our model is that it uses established knowledge as a reference to determine the direction of analyzing microarray dataset. In the most of previous work, only intrinsic information in the miroarray is used for the identifying DEGs. We hope that our proposed method could contribute to construct biologically meaningful network structure from microarray datasets.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2003.04a
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• pp.47-48
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• 2003

The development of cDNA microarray has permitted the analysis of thousands of genes simultaneously. cDNA microarray has been used to analyze gene expression profiles during developmental stage in both single and multicellular organisms. Two significant factors contributing to the limitation of the development of cDNA microarray in the Bombyx mori are the shortage of accessible repositories of cDNA clones and ESTs and the relative scarcity of facilities to produce microarrays and analyze the data generated. (omitted)

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.41-44
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• 2000

With the advent of DNA microarray and "chip" technologies, gene expression in an organism can be monitored on a genomic scale, allowing the transcription levels of many genes to be measured simultaneously. Functional interpretation of massive expression data and linking such data to DNA sequences have become the new challenges to bioinformatics. I will us yeast cell cycle expression data analysis as an example to demonstrate how special database and computational methods may be used for extracting functional information, I will also briefly describe a novel clustering algorithm which has been applied to the cell cycle data.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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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.

• Journal of Applied Biological Chemistry
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• v.55 no.4
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• pp.227-234
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• 2012

We observed that oil began to accumulate at 25 seed days after flowering (DAF) and reached the maximum potential at 35 seed DAF of oilseed rape, and the greatest weight of 100 seeds was obtained at 35 seed DAF. To survey a broad analysis of gene expression in developing embryos of Brassica napus, the Bn 300k microarray have been constructed. The Bn 300k Microarrary was designed from 80,696 unigenes clustered from 543,448 ESTs and 780 cDNA at NCBI. These arrays have been hybridized in a series of experiments with probes derived from seeds and leaf of B. napus. Approximately 8.5% of the 7,000 genes were expressed as ratios 2-fold higher in seed (25 DAF) than leaves and 0.4% at ratios 10. Also we observed that storage and cell differentiation-related genes were highly expressed at 10 DAF, whereas energy-related genes including fatty acid metabolism were increased up depending on seed maturation using Microarray, which was confirmed by reverse transcriptase polymerase chain reaction. These results suggest that B. napus arrays provide a very useful data set of seed-specific expression that can be further analyzed by examination of the promoter regions of these genes and help our understanding of the complex regulatory network in developing seeds.

• Journal of Life Science
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• v.22 no.11
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• pp.1552-1557
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• 2012

It has been reported that pipernonaline isolated from Piper longum Linn. has a wide biochemical and pharmacological effect, including antitumor activity in prostate cancer PC-3 cells. However, its mechanism and expression pattern of many genes involved in biological functions are not clearly understood. To perform the gene expression study in PC-3 cells treated with pipernonaline, a cDNA microarray chip composed of 44,000 human cDNA probes was used. As a result, cell cycle-related genes, apoptosis-related genes, and cell proliferation/growth-related genes have been identified in gene ontology of the DAVID database. These results suggest that pipernonaline has antitumor activity by regulating the expression pattern of genes involved in biological signaling pathway in prostate cancer PC-3 cells. Further, additional analysis of these microarray data can be a useful tool to identify the mechanism and discovery of novel genes in cancer therapy.

• Korean Journal of Microbiology
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• v.41 no.2
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• pp.105-111
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• 2005

Streptomyces produces many kinds of secondary-metabolites including antibiotics. Screening of a new compound and elucidation of a biosynthetic pathway for the secondary metabolites are very important fields of biology, however, there is a main problem that most of the identified compounds are already researched compounds. To solve these problems, a microarray system that is based on the data related to the biosynthetic genes for secondary-metabolites was designed. For the main contents of DNA microarray, the important genes for the bio-synthesis of aminoglycosides, polyenes group, enediyne group, alpha-glucosidase inhibitors, glycopeptide group, and orthosomycin group were chosen. A DNA microarray with 69 genes that were involved in the bio-synthesis for the antibiotics mentioned above was prepared. The usability of the DNA microarray was confirmed with the chromosomal DNA and total RNA extracted from S. coelicolor whose genomic sequence had already been reported.