• Molecular & Cellular Toxicology
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• 제1권2호
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• pp.92-98
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• 2005

DNA microarray analysis of gene expression in toxicogenomics typically requires relatively large amounts of total RNA. This limits the use of DNA microarray when the sample available is small. To confront this limitation, different methods of linear RNA amplification that generate antisense RNA (aRNA) have been optimized for microarray use. The target preparation strategy using amplified RNA in DNA microarray protocol can be divided into direct-incorporation labeling which resulted in cDNA targets (Cy-dye labeled cDNA from aRNA) and indirect-labeling which resulted in cRNA targets (i.e. Cy-dye labeled aRNA), respectively. However, despite the common use of amplified targets (cDNA or cRNA) from aRNAs, no systemic assessment for the use of amplified targets and bias in terms of hybridization performance has been reported. In this investigation, we have compared the hybridization performance of cRNA targets with cDNA targets from aRNA on a 10 K cDNA microarrays. Under optimized hybridization conditions, we found that 43% of outliers from cDNA technique and 86% from the outlier genes were reproducibly detected by both targets hybridization onto cDNA microarray. This suggests that the cRNA labeling method may have a reduced capacity for detecting the differential gene expression when compared to the cDNA target preparation. However, further validation of this discordant result should be pursued to determine which techniques possesses better accuracy in identifying truly differential genes.

• 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.

• 대한미생물학회지
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• 제35권4호
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• pp.299-308
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• 2000

Recently developed cDNA microarray or DNA chip technology allows expression monitoring of expression of hundreds and thousands of genes simultaneously and provides a format for identifying genes as well as changes in their activity. In order to search for changes in gene expression after X irradiation in HL60 cells, cDNA microarray technique was done. In this study, expression of 588 human genes (including oncogenes, tumor suppressor genes, cell cycle regulator genes, intracellular signal transduction modulator genes, apoptosis related genes, transcription factor genes, growth factors and receptor genes, cytokine genes, etc) were analyzed. For cDNA microarray analysis mRNAs were extracted from control and 8 Gy-irradiated HL60 cells. As a result the changes in expression of several genes were observed. This alteration of gene expression was confirmed by reverse transcription-polymerase chain reaction. The expression of heat shock 60 KD protein, c-jun, erythroid differentiation factor, CPP32, myeloid cell nuclear differentiation antigen, MAP kinase-activated protein kinase, interleukin-8, monocyte chemotactic peptide 1 and RANTES genes was increased, but the expression of p55CDC gene was decreased after X irradiation.

• 생물정신의학
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• 제7권2호
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• pp.123-130
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• 2000

The development of inexpensive high throughput methods to identify individual DNA sequences is important to the future growth of medical genetics. This has become increasingly apparent as psychiatric geneticists focus more attention on the molecular basis of complex multifactorial diseases at which most of psychiatric disease is estimated. Furthermore, candidate gene approaches used in identifying disease associated genes necessitate screening large sequence blocks for changes tracking with the disease state. Even after such genes are isolated, large scale mutational analysis will often be needed for risk assessment studies to define the likely medical consequences of carrying a mutated gene. This review provide basic knowledge of up-to-date technology, cDNA microarray which enables above mentioned various research themes.

• 한국환경독성학회:학술대회논문집
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• 한국환경독성학회 2003년도 추계국제학술대회
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• pp.173-173
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• 2003

With the introduction of DNA microarrays, a high throughput analysis of gene expression is now possible as a replacement to the traditional time-consuming Southern-blot analysis. This cDNA microarray should be ahighly favored technology in the area of molecular toxicology or analysis of environmental stresses.In this study, therefore, we developed a novel cDNA microarray for analyzing stress-specific responses in japanese Medaka fish. In the design and fabrication of this stress specific functional cDNA microarray, 123 different genes in Medaka fish were selected from eighteen different stress responsive groups and spotted on a 25${\times}$75 mm glass surface. After exposure of the fish to bisphenol A which is the one of the well-known endocrine disrupting chemicals (EDCs), over 1 or 10 days, the responses of the DNA chip were found to show distinct expression patterns according to the mode of toxic actions from environmental toxicants. As a results, they showed specific gene expression pattern to bisphenol A, additionally, the chemical spesific biomarkers could be suggested based on the chip analysis data. Therefore, this chip can be used to monitor stress responses of unknown and/or known toxic chemicals using Medaka fish and may be used for the further development of biomarkers by utilizing the gene expression patterns for known contaminants.

• 생명과학회지
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• 제25권4호
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• pp.376-384
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• 2015

소의 질을 평가하기 위해서는 중요한 인자인 근육내 지방(또는 마블링)을 조절하는 분자를 연구해야 한다. cDNA microarray를 사용하여 등지방 조직과 최장근의 유전자발현 차이를 비교하였다. 이 연구를 통해, 우리는 한우의 지방조직에 1211개, 근육조직에서 1346개의 특이 유전자를 확인하였다. bovine chip은 지방조직의 920개 유전자와 근육조직의 760개 유전자로 이루어진 1680개의 특이 유전자로 구성되어있다. 이 실험에서 Microarray 분석은 등지방조직(Cy3)과 최장근(Cy5)의 유전자 발현에 있어서 큰 차이를 보여준다. 차이를 보이는 많은 특이유전자 중에서, 12-리폭시게나아제 유전자와 프로스타글란딘 D 합성효소는 근육내 지방의 축적을 조절하는 중요한 효소이다. 본 연구에서, 일반적으로 발현되지만 한우의 근육과 지방 조직에서 차이를 보이는 많은 유전자를 hybridization 분석을 통해 발견하였다. 선택된 유전자의 발현 수준은 반정량적 RT-PCR을 통해 확인하였고, 그 결과는 cDNA microarray와 유사하였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.97-115
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• 2001

cDNA microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. Many statistical analysis tools become widely applicable to the analysis of cDNA microarray data. In this talk, we consider a two-way ANOVA model to differentiate genes that have high variability and ones that do not. Using this model, we detect genes that have different gene expression profiles among experimental groups. The two-way ANOVA model is illustrated using cDNA microarrays of 3,800 genes obtained in an experiment to search for changes in gene expression profiles during neuronal differentiation of cortical stem cells.

• 응용통계연구
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• 제22권3호
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• pp.617-626
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• 2009

최근에 보고되는 일련의 연구는 Affymetrix 마이크로어레이 자료에서 유전자간 상관관계가 강하고 장범위(長範圍)(long-ranged)로 나타나고 있으며, 기존의 "편한" 가정, 즉 유전자간 상관관계가 매우 약하며, 따라서 유전자간 유사 독립성을 가정할 수 있다는 주장이 비현실적이라는 것을 보고하고 있다. Qui 등 (2005b)은 각 유전자의 검정통계량을 병합하여 통계적 추론을 하는 이른바 비모수적 경험적 베이즈 방법을 적용하면 검색된 특이발현 유전자수의 분산이 커진다는 것을 보고하고 있고, 이러한 분산의 불안전성 이유로서 유전자간 강한 상관관계를 지적하고 있다. 또한 Klebanov와 Yakovlev (2007)는 유전자간 상관관계가 통계적 분석을 어렵게 하는 요인이라기 보다는 유용한 정보의 원천이고 적정한 변환을 통하여 근사 독립을 유지할 수 있는 급수를 만들 수 있으며 이 급수를 ${\delta}$-급수라고 불렀다. 본 보고에서는 국내에서 생산된 2조의 cDNA 마이크로어레이 자료에서 유전자간 상관관계가 비교적 강하며, 장범위(長範圍)로 나타나는 것을 확인하며, 유사 독립성을 전제할 수 있는 ${\delta}$-급수가 cDNA 마이크로어레이에서도 발견되는 것을 보고하고자 한다, 동 보고는 추후 cDNA 마이크로어레이 자료의 분석에서도 유전자간 상관관계를 고려하여야 함을 강조하고 있다.

• Asian-Australasian Journal of Animal Sciences
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• 제16권12호
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• pp.1837-1841
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• 2003

In an attempt to isolate novel molecules that may play a regulatory role in adipocyte differentiation, we devised an experimental strategy to identify adipose tissue-specific genes by modifying cDNA microarray technique. We used genefilter membranes containing approximately 15,000 rat non-redundant EST clones of which 4,000 EST were representative clones of known genes and 11,000 ESTs were uncharacterized clones. A series of hybridization of genefilter membranes with cDNA probes prepared from various rat tissues and nucleic acids sequence analysis allowed us to identify two adipose-tissue specific genes, adipocyte-specific secretory factor (ADSF) and H-rev107. Verification of tissue-specific expression patterns of these two genes by Northern blot analysis showed that ADSF mRNA is exclusive expressed in adipose tissue and the H-rev107 mRNA is predominantly expressed in adipose tissue. Further analysis of gene expression of ADSF and H-rev107 during 3T3-L1 adipocyte differentiation revealed that the ADSF and H-rev107 gene expression patterns are closely associated with the adipocyte differentiation program, indicating their possible role in the regulation of adipose tissue development. Overall, we demonstrated an application of modified cDNA microarray technique in molecular cloning, resulting in identification of two novel adipose tissue-specific genes. This technique will also be used as a useful tool in identifying novel genes expressed in a tissue-specific manner.