• 한국독성학회:학술대회논문집
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• 한국독성학회 2000년도 국제심포지움 및 추계학술대회
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• pp.31-41
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• 2000

The major issue in the post genome sequencing era is determination of gene expression patterns in variety of biological systems. A microarray system is a powerful technology for analyzing the expression profile of thousands of genes at one experiment. In this study, we constructed cDNA microarray which carries 2,304 cDNAS derived from oligo-capped mouse cDNA library. Using this hand-made microarray we determined gene expression in various biological systems. To determine tissue specific genes, we compared Nine genes were highly-expressed in adult mouse brain compared to kidney, liver, and skeletal muscle. Tissue distribution analysis using DNA microarray extracted 9 genes that were predominantly expressed in the brain. A database search showed that five of the 9 genes, MBP, SC1, HiAT3, S100 protein-beta, and SNAP25, were previously known to be expressed at high level in the brain and in the nervous system. One gene was highly sequence similar to rat S-Rex-s/human NSP-C, suggesting that the gene is a mouse homologue. The remaining three genes did not match to known genes in the GenBank/EMBL database, indicating that these are novel genes highly-expressed in the brain. Our DNA microarray was also used to detect differentiation specific genes, hormone dependent genes, and transcription-factor-induced genes. We conclude that DNA microarray is an excellent tool for identifying differentially expressed genes.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.98-107
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• 2006

Chromosomal copy number changes (aneuploidies) are common in human populations. The extra chromosome can affect gene expression by whole-genome level. By gene expression microarray analysis, we want to find aberrant gene expression due to aneuploidies in Klinefelter (+X) and Down syndrome (+21). We have analyzed the inactivation status of X-linked genes in Klinefelter Syndrome (KS) by using X-linked cDNA microarray and cSNP analysis. We analyzed the expression of 190 X-linked genes by cDNA microarray from the lymphocytes of five KS patients and five females (XX) with normal males (XY) controls. cDNA microarray experiments and cSNP analysis showed the differentially expressed genes were similar between KS and XX cases. To analyze the differential gene expressions in Down Syndrome (DS), Amniotic Fluid (AF)cells were collected from 12 pregnancies at $16{\sim}18$ weeks of gestation in DS (n=6) and normal (n=6) subjects. We also analysis AF cells for a DNA microarray system and compared the chip data with two dimensional protein gel analysis of amniotic fluid. Our data may provide the basis for a more systematic identification of biological markers of fetal DS, thus leading to an improved understanding of pathogenesis for fetal DS.

• 동의신경정신과학회지
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• 제18권1호
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• pp.95-110
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• 2007

Objective : The purpose of this study was to investigate molecular basis of neuroprotective effect in total ginsenosides. After H202 induced neurotoxicity, gene expression profiling of SH-SY5Y neuroblastoma cells treated by total ginsenosides is analyzed. Method : After SH-SY5Y cells were cultured, they were damaged by H202 induced oxidative stress. After twenty four hours, experimental group is treated by total ginsenosides and control group is treated by 0.9% saline. A high density cDNA microarray chip is used to analyze the gene expression profiling of SH-SY5Y cells. The Significance Analysis of Microarray method is used for identifying genes on a microarray. Results : 1. According to the results of microarray experiment, 17 genes were up-regulated, 38 genes were down-regulated. 2. Expression of OPHNl, KTANl, ATM, PRKCE, MAPKs genes associated with cell proliferation, neural growth, and the prevention of apoptosis were increased. 3. Change of EPX gene was the greatest among all genes. EPX gene associated with oxidative stress, and tumor suppressor gene ADAM11 were decreased. Conclusion : According to this study, molecular basis of neuroprotective effect of total ginsenosides is as followings: the increase of gene expression associated with cell proliferation, neuron growth, the prevention of apoptotsis and decrease of gene expression associated with oxidative stress and tumor suppressor.

• 한국데이터정보과학회:학술대회논문집
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• 한국데이터정보과학회 2005년도 추계학술대회
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• pp.153-159
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• 2005

Microarray gene expression technology has applications that could refine diagnosis and therapeutic monitoring as well as improve disease prevention through risk assessment and early detection. Especially, microarray expression data can provide important information regarding specific genes related with metastasis through an appropriate analysis. Various methods for clustering analysis microarray data have been introduced so far. We used twostep clustering fot ascertain metastasis related gene through t-test. Through t-test between two groups for two publicly available medulloblastoma microarray data sets, we intended to find significant gene for metastasis. The paper describes the process in detail showing how the process is applied to clustering analysis and t-test for microarray datasets and how the metastasis-associated genes are explorated.

• Genomics & Informatics
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• 제3권1호
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• pp.39-42
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• 2005

DNA microarray is a high-throughput biomedical technology that monitors gene expression for thousands of genes in parallel. The abundance and complexity of the gene expression data have given rise to a requirement for their systematic management and analysis to support many laboratories performing microarray research. On these demands, we developed Xperanto for integrated data management and analysis using user-friendly web-based interface. Xperanto provides an integrated environment for management and analysis by linking the computational tools and rich sources of biological annotation. With the growing needs of data sharing, it is designed to be compliant to MGED (Microarray Gene Expression Data) standards for microarray data annotation and exchange. Xperanto enables a fast and efficient management of vast amounts of data, and serves as a communication channel among multiple researchers within an emerging interdisciplinary field.

• Journal of Information Processing Systems
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• 제19권5호
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• pp.652-662
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• 2023

Identifying highly discriminating genes is a critical step in tumor recognition tasks based on microarray gene expression profile data and machine learning. Gene selection based on tree models has been the subject of several studies. However, these methods are based on a single-tree model, often not robust to ultra-highdimensional microarray datasets, resulting in the loss of useful information and unsatisfactory classification accuracy. Motivated by the limitations of single-tree-based gene selection, in this study, ensemble gene selection methods based on multiple-tree models were studied to improve the classification performance of tumor identification. Specifically, we selected the three most representative tree models: ID3, random forest, and gradient boosting decision tree. Each tree model selects top-n genes from the microarray dataset based on its intrinsic mechanism. Subsequently, three ensemble gene selection methods were investigated, namely multipletree model intersection, multiple-tree module union, and multiple-tree module cross-union, were investigated. Experimental results on five benchmark public microarray gene expression datasets proved that the multiple tree module union is significantly superior to gene selection based on a single tree model and other competitive gene selection methods in classification accuracy.

• 유전체소식지
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• 제6권1호
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• pp.29-33
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• 2006

Gene set analysis is a new concept and method. to analyze and interpret microarray gene expression data and tries to extract biological meaning from gene expression data at gene set level rather than at gene level. Compared with methods which select a few tens or hundreds of genes before gene ontology and pathway analysis, gene set analysis identifies important gene ontology terms and pathways more consistently and performs well even in gene expression data sets with minimal or moderate gene expression changes. Moreover, gene set analysis is useful for comparing multiple gene expression data sets dealing with similar biological questions. This review briefly summarizes the rationale behind the gene set analysis and introduces several algorithms and tools now available for gene set analysis.

• KSBB Journal
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• 제20권3호
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• pp.220-227
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• 2005

독소루비신 생합성 유전자의 발현을 촉진시키는 유전자인 dnrI와 다나루비신으로부터 독소루비신으로의 생전환에 관여하는 유전자인 doxA를 ermE 프로모터가 포함된 pSE34에 도입하였을 때 각각 5.5배, 2.5배의 독소루비신 생산성 증가가 이루어졌다. 독소루비신 생합성 유전자군의 발현패턴 분석을 위한 DNA microarray system을 구축하였고, 고생산 균주의 독소루비신 생합성 유전자 발현 패턴을 DNA microarray를 통해 확인하였다. 독소루비신 생합성 유전자군의 세포성장에 따른 발현패턴을 분석한 결과, 독소루비신 생산성 증가에 따라 생합성 유전자의 발현도 증가함을 확인할 수 있었고, pSE34를 통해 도입해준 donA, dnrI 유전자의 경우 전체 생합성 유전자의 평균보다 높은 수준의 발현량을 보여줌으로써, ermE 프로모터에 의해 발현이 극대화되었음을 확인할 수 있었다. 독소루비신 내성 유전자의 경우 다른 독소루비신 생합성 유전자들에 비해 발현정도가 크게 증가했고, DnrI 의해 조절을 받는 다른 유전자들의 발현 수준과 비교하였을 때 TDP-daunosamine을 생합성의 첫 번째 단계에 관여하는 dnmL 유전자는 그 발현양의 증가가 크지 않았다. 따라서 DNA microarray 시스템 분석 결과, 독소루비신 생산성 극대화를 위해서는 dnrI, doxA, drrA, drrB, drrC, dnmL 등의 유전자들의 안정적 발현이 매우 중요하고도 핵심적인 인자임이 확인되었다.

• Communications for Statistical Applications and Methods
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• 제11권1호
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• pp.59-77
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• 2004

Since the introduction of DNA microarray, a revolutionary high through-put biological technology, a lot of papers have been published to deal with the analyses of the gene expression data from the microarray. In this paper we review most papers relevant to the cDNA microarray data, classify them in statistical methods' point of view, and present some statistical methods deserving consideration and future study.

• Molecular & Cellular Toxicology
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• 제5권1호
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• pp.44-50
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• 2009

This study was conducted to evaluate the inflammation mechanisms of tumor necrosis factor-$\alpha$ (TNF-$\alpha$), interleukin-4 (IL-4), and IL-$1{\beta}$-induced stimulation of A549 human epithelial cells. In the present study, A549 cells were stimulated with TNF-$\alpha$, IL-4 and IL-$1{\beta}$ to induce expression of chemokines and adhesion molecules involved in eosinophil chemotaxis. The effects of TNF-$\alpha$, IL-4 and IL-$1{\beta}$ on gene expression profiles in A549 cells were evaluated by oligonucleotide microarray and Real time RT-PCR. The gene expression profiles for the A549 cells varied depending on the cytokines. Also, the results of the microarray and Real time RT-PCR revealed that inflammatory-related genes were up-regulated in cytokine stimulated A549 cells. Cytokines can affect inflammation in A549 cells. A microarray-based genomic survey is a high-throughput approach that enables evaluation of gene expression in cytokine stimulated cell lines.