• The Korean Journal of Nuclear Medicine
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• v.37 no.1
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• pp.43-52
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• 2003

Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen loading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with ceil lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA In fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high qualify rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. in summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most practical experimental approach in studying psychiatric and neurodegenerative disorders, and other complex questions in the brain.

• Journal of Embryo Transfer
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• v.25 no.1
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• pp.29-34
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• 2010

Follicular cystic ovary (FCO) is one of the major causes of reproductive failure in cattle. Genetic alterations affect the function of diverse cells and/or tissues, which could be present in cystic ovaries. A microarray analysis was performed to screen differential gene expressions in follicular cystic follicles of cattle. In this study, we hypothesized that follicular cysts may be induced by changes in ion- and transporter-related gene expression. Microarray data showed that fibrinogen-gamma (FGG) and low density lipoprotein receptor-related protein 8 (LRP8) were up-regulated, while choline transporter-like protein 4 (SLC44A4), very long-chain acyl-CoA synthetase homolog 2 (SLC27A5), annexin 8 (ANXA8), and aquaporin 4 were down-regulated in follicular cystic follicles. A semi-quantitative RT-PCR was carried out to validate DEGs altered in follicular cystic follicles. Of six DEGs, three DEGs (FGG, SLC44A4, and aquaporin 4) showed a positive correlation between microarray and semi-quantitative PCR data. We focused on FGG, among three DEGs, which was highly up-regulated in follicular cystic follicles. The FGG mRNA was upregulated by 8.4-fold and by 1.7-fold in the bovine follicular cystic follicles as judged by microarray and RT-PCR analysis, respectively. However, there was no significant changes in the expression level of FGG protein in both follicular cystic follicles and granulosa cells isolated from follicular cystic follicles by Western blot analysis. Although this study does not reveal a positive correlation between the mRNA and protein level, FGG appears to be an important biomarker in the discrimination of follicular cyst from normal ovary.

• Journal of Physiology & Pathology in Korean Medicine
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• v.17 no.6
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• pp.1393-1403
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• 2003

The genetic effects of restraint stress challenge on HPA axis and the therapeutic effect of Boshimgeonbi-Tang on the stress were studied with cDNA microarray analyses on hypothalamus using an immobilization-stress mouse as stress model. Male CD-1 mice were restrained in a tightly fitted and ventilated vinyl holder for 2hours once a day, and this challenge was repeated for seven consecutive days. The body weights of the immobilization-stress mice were diminished about 25 percent degree as compared to normal ones. Seven days later, total RNA was extracted from the organs of the mouse, body-labeled with CyDye/sup TM/ fluorescence dyes (Amersham Bioscience Co., NJ), and then hybridized to cDNA microarray chip. Scanning and analyzing the array slides were carried out using GenePix 4000 series scanner and GenePix Pro/sup TM/ analyzing program, respectively. The expression profiles of 109 genes out of 6000 genes on the chip were significantly modulated in hypothalamus by the immobilization stress. Energy metabolism-, lipid metabolism-, apoptosis- and signal transduction-related genes were transcriptionally activated whereas DNA repair-, protein biosynthesis-, and structure integrity-related genes were down-regulated in hypothalamus. The 58 genes were up-regulated by the mRNA expression folds of 1.5 to 7.9. and the 51 genes were down-regulated by 1.5 - 3.5 fold. The 20 genes among them were selected to confirm the expression profiles by RT-PCR. The mRNA expression levels of Tnfrsf1a (apoptosis), Calm2 (cell cycle), Bag3 (apoptosis), Hspe1 (protein folding), Aatk (apoptosis), Dffa (apoptosis), Itgb1 (cell adhesion), Vcam1 (cell adhesion), Fkbp5 (protein folding), BDNF (neuron survival) were restored to the normal one by the treatment of Boshimgeonbi-Tang.

• Journal of Periodontal and Implant Science
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• v.36 no.3
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• pp.767-782
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• 2006

이 연구의 목적은 DNA microarray 분석법을 이용하여 건강한 사람치주인대섬유모세포, 건강한 사람치은섬유모세포, 복제노화된 사람치은섬유모세포, 염증성 사람치주인대 섬유모 세포의 유전자 발현 형태를 상호비교하고자 하였다. 환자의 동의하에 충치, 치주염이 없이 교정발치된 치아의 치주인대세포를 배양하여 건강한 치주인대섬유모세포로, 만성치주염으로 발거된 치아에서 채취하여 배양한 세포를 염증성 치주인대섬유모세포로 선정하였다. 구강에서 채취한 치은결체조직에서 배양한 사람치은섬유모세포를 일차 배양한 후 계대배양을 통해 복제 노화를 유도하였다. $-198^{\circ}C$의 액화질소에 저장되어 있던 2, 4, 8, 15, 16세대 세포를 실험에 이용하였다. 위의 모든 세포들은 60 mm 배양접시에서 세포들이 80-90%의 밀생이 될 때까지 5% $CO_2$, $37^{\circ}C$, 100% 습도의 배양기에서 2일 간격으로 10% FBS가 함유된 DMEM 세포 배양액을 교체하면서 세포를 배양하였다. Trizol Reagent (Invitrogen, USA)를 이용하여 제조회사의 지시에 따라 total RNA를 추출하였다. 18S RNA와 28S RNA를 확인한 후 DNA microarray 분석을 실시하였다. 4배수 이상의 변화양상을 비교시 상호 유전자 발현의 차이를 나타내었다. 건강한 사람치은섬유모세포(2세대)와 노화된 치은섬유모세포에서 가장 높은 발현변화를 나타낸 반면 DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination,은 건강한 치은섬유모세포에서 가장 높게 나타났다. 염증성 치은인대섬유모세포와 건강한 치주인대 섬유모세포를 비교시, Regucalcin은 염증성 치주인대섬유모세포에서 가장 높게 나타났고, Vascular cell adhesion molecule 1도 두 번째로 높게 나타났다. 건강한 치주인대섬유모 세포와 건강한 치은섬유모세포를 비교시, IL-11과 periostin이 치주인대섬유모세포에서 높은 발현을 나타낸 반면, Prostaglandin D2 synthase 21kDa과 Thioredoxin interacting protein은 치은섬유모세포에서 높은 발현을 나타내었다. 염증성 치주인대섬유모세포와 노화된 치은섬유모세포(15세대 이상)를 비교시 149개의 유전자가 유사한 발현 수준을 나타내었다. 이 연구는 노화, 염증, 세포 형태에 따라서 유전자 수준에서 가장 높거나 높은 수준 변화를 보이는 유전자가 다를 수 있음을 나타낸다. 향후, 치주염 환자들에서, 노염, 염증, 세포 특이성에 관한 유전자 표시지를 이용하여 진단하거나 치료에 응용하기 위해서는 더 많은 연구가 필요하리라 사료된다.

• Journal of Life Science
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• v.18 no.1
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• pp.75-83
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• 2008

This studies were designed to elucidate whether inhibitors of topoisomerase regulate function and activity of topoisomerase, and gene expression in HL-60 human leukemia cells. HL-60 cells were treated with 10-hydroxycamptothecin or doxorubicin, total RNA was isolated, and expressed genes were investigated with human oligonucleotide microarray containing 10K gene, respectively. Expression profiles of the human leukemia HL-60 cells treated with 10-hydroxycamptothecin (10-CIT) or doxorubicin associated with signal transduction,. cell adhesion, cell cycle, cell growth, cell proliferation, cell differentiation, transcription and immune response, especially genes related with transcription and cell growth. In HL-60 cells treated with 10-CPT, the expression of topoisomerase III${\alpha}$, III${\beta}$ and I gene from oligo chip microarray analysis were increased over, but the expression of topoisomerase II${\alpha}$ and II${\beta}$ gene were decreased over. In contrast, the expression of topoisomerase II${\alpha}$ and II${\beta}$ gene were increased over in HL-60 cells treated with doxorubicin, whereas the expression of topoisomerase III${\alpha}$ and III${\beta}$ mRNA remained no significant change. These results suggest that these data may be useful for novel therapeutic markers.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.20-28
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• 2006

최근의 microarray 기술의 발달로 인해 점점 더 많은 양의 mRNA 발현 데이터가 쌓여 가고 있다. 이제는 데이터를 만드는 단계보다는 데이터로부터 중요한 생물학적 의미를 끌어내는 것이 더욱 중요한 일이 되었다. micorarray 기술이 처음 도입된 이후로, 많은 앨고리즘과 소프트웨어가 개발되어, 실험자들이 microarray 데이터로부터 생물학적 의미를 끌어내는 작업을 도와주어 왔다. 그런데, 이전의 데이터 마이닝 방법들은 거의 예외 없이 전체 데이터로부터 선택된 몇 십, 몇 백 개의 유전자 리스트로부터 출발한다. 그런데, 이러한 방법 (over-representation analysis, ORA로 줄임)은 몇 가지 한계를 가지고 있어서, 최근에는 전체 데이터로부터 의미 있는 유전자 세트 (gene set)를 찾아내는 방법들이 도입되었다. 본 세미나는 이런 방법들, 줄여서 gene set analysis라 함, 에 사용되는 앨고리즘들과 소프트웨어들을 비교, 검토하고자 한다.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.13-15
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• 2006

microRNA는 유전자의 전사 후 과정에서 negative regulation을 담당하는 small noncoding RNA의 한 증류이다. 최근까지 330여개의 인간 microRNA가 발견되었지만 그들의 기능이 밝혀진 것은 소수에 불과하다. microRNA의 기능은 3'UTR에 불완전 상보결합을 통해 negative regulation을 받게 되는 유전자의 기능으로부터 유추되는 것이 일반적이다. 특별히 유전체상에 군집화 된 microRNA들은 하나의 전사체로부터 발현되는 것으로 판단되며, 같은 또는 관련된 기능을 하거나 같은 목표 유전자를 조절하기 위한 functional family일 가능성이 높다. 또한 이러한 functional family는 하나의 전사체로부터 발현되기 때문에, 조직별로 조건별로 같은 발현 패턴을 보여야 한다. 본 연구에서는 발현데이터로부터 microRNA functional family를 탐색하기 위해, 5개의 연구 그룹에서 공개한 조직별 microRNA 발현데이터를 표준화 작업을 거친 후 통합하고 k-nearest neighbor 알고리즘을 이용해 결측치를 보정한 후 microRNA 발현사이의 correlation을 계산한다. 이때 데이터 통합에서 생기는 문제에 robust한 결과를 얻기 위해 실제 발현데이터가 아닌 rank 데이터부터 correlation을 측정한다. 계산된 spearman ranked correlation 결과와 microRNA의 genomic coordination 정보로부터 34개의 functional family를 정의할 수 있었다.

• Restorative Dentistry and Endodontics
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• v.37 no.3
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• pp.142-148
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• 2012

Objectives: We analyzed gene-expression profiles after 14 day odontogenic induction of human dental pulp cells (DPCs) using a DNA microarray and sought candidate genes possibly associated with mineralization. Materials and Methods: Induced human dental pulp cells were obtained by culturing DPCs in odontogenic induction medium (OM) for 14 day. Cells exposed to normal culture medium were used as controls. Total RNA was extracted from cells and analyzed by microarray analysis and the key results were confirmed selectively by reverse-transcriptase polymerase chain reaction (RT-PCR). We also performed a gene set enrichment analysis (GSEA) of the microarray data. Results: Six hundred and five genes among the 47,320 probes on the BeadChip differed by a factor of more than two-fold in the induced cells. Of these, 217 genes were upregulated, and 388 were down-regulated. GSEA revealed that in the induced cells, genes implicated in Apoptosis and Signaling by wingless MMTV integration (Wnt) were significantly upregulated. Conclusions: Genes implicated in Apoptosis and Signaling by Wnt are highly connected to the differentiation of dental pulp cells into odontoblast.

• BMB Reports
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• v.39 no.3
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• pp.247-252
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• 2006

A rapid method for the detection of Hepatitis E Virus (HEV) was developed by utilizing nano-gold labeled oligonucleotide probes, silver stain enhancement and the microarray technique. The 5'-end -$NH_2$ modified oligonucleotide probes were immobilized on the surface of the chip base as the capture probe. The detection probe was made of the 3'-end -SH modified oligonucleotide probe and nano-gold colloid. The optimal concentrations of these two probes were determined. To test the detection sensitivity and specificity of this technique, a conservative fragment of the virus RNA was amplified by the RT-PCR/PCR one step amplification. The cDNA was hybridized with the capture probes and the detection probes on microarray. The detection signal was amplified by silver stain enhancement and could be identified by naked eyes. 100 fM of amplicon could be detected out on the microarray. As the results, preparation of nano-gold was improved and faster. Development time also was shortened to 2 min. Thus, considering high efficiency, low cost, good specificity and high sensitivity, this technique is alternative for the detection of HEV.

• The Korean Journal of Physiology and Pharmacology
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• v.10 no.4
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• pp.173-180
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• 2006

Microglial activation is thought to play a role in the pathogenesis of many brain disorders. Therefore, understanding the response of microglia to noxious stimuli may provide insights into their role in disorders such as stroke and neurodegeneration. Many genes involved in this response have been identified individually, but not systematically. In this regards, the microarray system permitted to screen a large number of genes in biological or pathological processes. Therefore, we used microarray technology to evaluate the effect of oxygen glucose deprivation (OGD) and reperfusion on gene expression in microglia under ischemia-like and activating conditions. Primary microglial cultures were prepared from postnatal mice brain. The cells were exposed to 4 hrs of OGD and 1 h of reperfusion at $37^{\circ}C$. Isolated mRNA were run on GeneChips. After OGD and reperfusion, ＞2-fold increases of 90 genes and ＞2-fold decrease of 41 genes were found. Among the genes differentially increased by OGD and reperfusion in microglia were inflammatory and immune related genes such as prostaglandin E synthase, $IL-1{\beta}$, and $TNF-{\alpha}$. Microarray analysis of gene expression may be useful for elucidating novel molecular mediators of microglial reaction to reperfusion injury and provide insights into the molecular basis of brain disorders.