• 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.

• 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.

• 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.

• 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.

• 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.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2001년도 추계학술발표대회
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• pp.739-740
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• 2001

37종의 주요 대사관련 유전자를 triplicate로 사용하여 DNA microarray를 제작하여 라이신 생산균주의 포도당과 원당을 탄소원으로 하여 배양시기에 따른 대사특성을 분석하였다. 포도당과 원당 사용시 C3, C4 대사산물의 변환에 관련된 anaplerosis에 관여하는 유전자의 발현변화가 매우 중요함을 파악할 수 있었다. 또한 배양시기에 따라 매우 특이적인 유선자 발현 양상을 보임을 학인할 수 있었다.

• 한국데이터정보과학회:학술대회논문집
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• 한국데이터정보과학회 2006년도 PROCEEDINGS OF JOINT CONFERENCEOF KDISS AND KDAS
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• pp.121-129
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• 2006

Two color or cDNA microarrays are extensively used to study relative expression levels of thousands of genes simultaneously. 0かy two tissue samples can be hybridized on a single microarray slide. Thus, a microarray slide necessarily forms an incomplete block design with block size two when more than two tissue samples are under study. We also need to control for variability in gene expression values due to the two dyes. Thus, red and green dyes form the second blocking factor in addition to slides. General design problem for these microarray experiments is discussed in this paper. Designs for factorial cDNA microarrays are also discussed.

• 한국통계학회:학술대회논문집
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• 한국통계학회 2002년도 춘계 학술발표회 논문집
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• pp.79-83
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• 2002

Since its introduction in 1995 by Schena et al. cDNA microarrays have been established as a potential tool for high-throughput analysis which allows the global monitoring of expression levels for thousands of genes simultaneously. One of the characteristics of the cDNA microarray data is that there is inherent noise even after the removal of systematic effects in the experiment. Therefore, replication is crucial to the microarray experiment. The assessment of reproducibility among replicates, however, has drawn little attention. Reproducibility may be assessed with several different endpoints along the process of data reduction of the microarray data. We define the reproducibility to be the degree with which replicate arrays duplicate each other. The aim of this note is to develop a novel measure of reproducibility among replicates in the cDNA microarray experiment based on the unprocessed data. Suppose we have p genes and n replicates in a microarray experiment. We first develop a measure of reproducibility between two replicates and generalize this concept for a measure of reproducibility of one replicate against the remaining n-1 replicates. We used the rank of the outcome variable and employed the concept of a measure of tracking in the blood pressure literature. We applied the reproducibility measure to two sets of microarray experiments in which one experiment was performed in a more homogeneous environment, resulting in validation of this novel method. The operational interpretation of this measure is clearer than Pearson's correlation coefficient which might be used as a crude measure of reproducibility of two replicates.

• 대한한의학회지
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• 제24권2호
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• pp.148-158
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• 2003

Backgrounds & Objectives: In many recent studies, molecular biological methods have been used to investigate the role of cytokines in pathogenesis and new therapeutic targets of asthma. Recently, as a method of research on the gene expression, they are applying another method which assays multiple gene expressions at the same time by the microarray. In this study, the antioxidant effect, the inhibitory effect against interleukin-4 and the effect on the CD/cytokine gene expression in PBMC (peripheral blood mononuclear cells) was evaluated by using cDNA microarray chip of Chungsangboha-tang. Methods: Experimental studies were performed for the antioxidant effect of Chungsangboha-tang on DPPH (1, 1-diphenyl-2-picrylhydrazyl) solution, for the IL-4-inhibiting effect on BALB/c mouse spleen, and for the gene expression effect on PBMC (peripheral blood mononuclear cells) with microarray. Results: Chungsangboha-tang showed antioxidant effect dose-dependently. Chungsangboha-tang inhibited interleukin-4 dose-dependently and showed significant difference in 10ug/ml and 100ug/ml of test groups. There was no 2 more times upregulated genes than in the control group by using cDNA microarray chip of Chungsangbohn-tang, but there were 140%-200% upregulated genes. There was no 2 more times downregulated genes than in the control group by using cDNA microarray chip of Chungsangboha-Tang, but there was 50%-75% downregulated genes. Conclusions: This study showed that Chungsangboha-tang has an antioxidant effect and inhibition of Interleukin-4, but further studies are necessary with microarray.