• Asian Pacific Journal of Cancer Prevention
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• 제17권5호
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• pp.2519-2525
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• 2016

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

• 동의생리병리학회지
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• 제24권5호
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• pp.831-836
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• 2010

In addition to spice, black pepper (Piper nigrum Linne : PnL) has been used as herbal medicine because of its function in anti-oxidation, anti-inflammation, and anti-carcinogenesis. Recently, it has been reported that piperine, a component of PnL, inhibits adipocyte differentiation by repressing various adipogenic gene expressions. In this study, we determined whether piperine is a major constituent of PnL that confers the anti-adipogenic activity at whole genome level. Differentiation of 3T3-L1 pre-adipocytes was induced in presence of PnL extract or piperine. To compare genes that are regulated by PnL extract or piperine, we performed expression profiling using microarrays (Agilent Mouse 44k 4plex). RNA samples were labeled with Cy3 and Cy5, respectively. Labeled samples were hybridized to the microarrays. Results were filtered and cut off set p<0.05. Genes exhibiting significant differences in expression level were classified into Gene Ontology (GO)-based functional categories (http://www.geneontology.org) and KEGG (http://www.genome.jp/kegg/). Extract of PnL and its component piperine reduced lipid accumulation in 3T3-L1 cells during adipogenesis. Such anti-adipogenic activity appears to result from down-regulation of transcription factor genes involved in adipogenesis, and other genes involved in fatty acid synthesis, transport, triglyceride synthesis, and carbohydrate metabolism. These genome-wide studies lead to conclude that piperine, as a critical component of PnL, plays common role with PnL in anti-adipogenesis.

• 한국미생물·생명공학회지
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• 제31권2호
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• pp.182-190
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• 2003

마이크로어레이 기술이 널리 이용됨에 따라 마이크로어레이 이미지 데이터와 이미지 분석 데이터들이 급격히 늘어나고 있다. 그러나 국내에서는 그 데이터들을 효율적으로 관리하기 위한 시스템이 개발되어 공개된 경우가 없다. 그리고 마이크로어레이 실험은 한 실험실에서 분석하고 연구할 수 있는 유전자의 수가 제한되어 있으므로 서로 다른 연구실에서 실험한 연구 결과들을 공유함으로써 실험의 중복을 막을 수 있고 그 연구 결과들을 축척할 수 있다. 본 논문에서는 마이크로어레이 이미지 데이터를 처리 및 관리하기 위한 통합 시스템, WEMA(Web management of MicroArray)를 개발하였다. WEMA는 마이크로어레이 데이터 표준 규정의 제안인 MIAME(Minimal Information About a Microarray Experiment)에서 정의한 데이터 요소를 바탕으로 데이터 스키마를 설계하였으며 마이크로어레이 실험 설계에 따라 체계적으로 데이터를 관리하기 위해서 공동적인 데이터 단위를 정의하였다. WEMA의 주요 기능은 마이크로어레이 이미지 및 분석 데이터의 효율적인 관리, 데이터입출력의 통합 기능, 메타 파일 생성 등이다. 본 WEMA 시스템을 이용해서 실제로 한 식물 분자 생물학 연구실에서 만들어내는 마이크로어레이 이미지 데이터를 처리, 관리한 결과 생물학자들이 마이크로어레이 데이터를 체계적으로 관리, 분석할 수 있었으며 연구자들간의 데이터 교환 및 의사 소통이 원활히 이루어졌다.

• Journal of Microbiology and Biotechnology
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• 제17권11호
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• pp.1826-1832
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• 2007

We describe the fabrication of poly(ethylene glycol) diacrylate (PEG-DA) hydrogel microstructures with a high aspect ratio and the use of hydrogel microstructures containing the enzyme ${\beta}$-galactosidase (${\beta}$-Gal) or glucose oxidase (GOx)/horseradish peroxidase (HRP) as biosensing components for the simultaneous detection of multiple analytes. The diameters of the hydrogel microstructures were almost the same at the top and at the bottom, indicating that no differential curing occurred through the thickness of the hydrogel microstructure. Using the hydrogel microstructures as microreactors, ${\beta}$-Gal or GOx/HRP was trapped in the hydrogel array, and the time-dependent fluorescence intensities of the hydrogel array were investigated to determine the dynamic uptake of substrates into the PEG-DA hydrogel. The time required to reach steady-state fluorescence by glucose diffusing into the hydrogel and its enzymatic reactions with GOx and HRP was half the time required for resorufin ${\beta}$-D-galactopyranoside (RGB) when used as the substrate for ${\beta}$-Gal. Spatially addressed hydrogel microarrays containing different enzymes were micropatterned for the simultaneous detection of multiple analytes, and glucose and RGB solutions were incubated as substrates. These results indicate that there was no cross-talk between the ${\beta}$-Gal-immobilizing hydrogel micropatches and the GOx/HRP-immobilizing micropatches.

• 한국한의학연구원논문집
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• 제6권1호
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• pp.89-98
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• 2000

Cerebral ischemia, the most prevalent form of clinical stroke, is a medical problem of the first magnitude. Substantial efforts are being made to develop drugs which will protect the brain from the neurodegeneration followed by an ischemic stroke. A key factor in this process is the development of animal models that mimic the neuropathological consequences of stroke. Recently, there is increasing an evidence that free radical is involved in the mechanisms of ischemic brain damage. We investigated the macro scale gene expression analysis on the global ischemia induced by 4-vessel occlusion in Wister rats. The recent availability of microarrays provides an attractive strategy for elaborating an unbiased molecular profile of large number of genes during ischemic injury. This experimental approach offers the potential to identify molecules or cellular pathways not previously associated with ischemia. Ischemia was induced by 4-vessel occlusion for 10 minutes and reperfused again. RNA from sham control brain and time-dependent ischemed brain were hybridized to microarrays containing 4,000 rat genes. 589 genes were found to be at least 2 fold regulated at one or more time points. These survey data provide the foundation studies that should provide convincing proof for ischemia and oxidative stress on gene expression.

• 한국한의학연구원논문집
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• 제8권2호통권9호
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• pp.95-107
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• 2002

Yukmijihwang-tang(YM) is a noted herbal prescription in Chinese and Korean traditional medicines, and it has been known to reinforce the vital essence and has been widely used for a variety of disease such as stroke, osteoporosis, anti-tumor, and hypothyrodism. Regarding its traditional use, YM has been known to reinforce the Yin (vital essence) of liver and kidney. Also it has been known to reinforce nutrition and biological function in brain. Recently, studies suggested that YM increase antioxidant activities and exert the protective effect against oxidant-induced liver cell injury. We investigated the high-throughput gene expression analysis on the Yukmijihwang-tang administrated in SD rats. Microarray data were validated on a limited number of genes by semiquantitative RT-PCR and Western blot analyses. The recent availability of microarrays provides an attractive strategy for elaborating an unbiased molecular profile of large number of genes in drug discovery This experimental approach offers the potential to identify molecules or cellular pathways not previously associated with herbal medicine. Total RNA from normal control brain and Yukmijihwang-tang administrated brain were hybridized to microarrays containing 10,000 rat genes. The 52 genes were found to be up-regulated(twice or more) excluding EST gene. The nine genes were found to be down-regulated(twice or more) excluding EST gene. Gene array technology was used to identify for the first time many genes expression pathway analysis that arecell cycle pathway, apoptosis pathway, electron transport chain pathway, cytoplasmic ribosomal protein pathway, fatty acid degradation pathway, and TGF-beta signaling pathway. These differentially expressed genes pathway analysis have not previously been iavestigated in the context of herbal medicine efficacy and represent novel factors for further study of the mechanism of herbal medicine efficacy.

• Journal of Plant Biotechnology
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• 제37권2호
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• pp.144-152
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• 2010

As the International Rice Genome Sequencing Project (IRGSP) was completed in 2005 and opened to the public, many countries are making a lot of investments in researches on the utilization of sequence information along with system development. Also, the necessity of the functional genomics researches using microarray is increased currently to secure unique genes related with major agricultural traits and analyze metabolic pathways. Microrarray enables efficient analysis of large scale gene expression and related transcription regulation. This review aims to introduce available microarrays made based on rice genome information and current status of gene expression analysis using these microarrays integrated with the databases available to the public. Also, we introduce the researches on the large scale functional analysis of genes related with useful traits and genetic networks. Understanding of the mechanism related with mutual interaction between proteins with co-expression among rice genes can be utilized in the researches for improving major agricultural traits. The direct and indirect interactions of various genes would provide new functionality of rice. The recent results of the various expression profiling analysis in rice will promote functional genomic researches in plants including rice and provide the scientists involved in applications researches with wide variety of expression informations.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2005년도 총회 및 춘계학술발표회
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• pp.28-30
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• 2005

Because of high population diversity in soil microbial communities, it is difficult to accurately assess the capability of biodegradation of toxicant by microbes in soil and sediment. Identifying biodegradative microorganisms is an important step in designing and analyzing soil bioremediation. To remove non-important noise information, it is necessary to selectively enrich genomes of biodegradative microorganisms fromnon-biodegradative populations. For this purpose, a stable isotope probing (SIP) technique was applied in selectively harvesting the genomes of biphenyl-utilizing bacteria from soil microbial communities. Since many biphenyl-using microorganisms are responsible for aerobic PCB degradation In soil and sediments, biphenyl-utilizing bacteria were chosen as the target organisms. In soil microcosms, 13C-biphenyl was added as a selective carbon source for biphenyl users, According to $13C-CO_2$ analysis by GC-MS, 13C-biphenyl mineralization was detected after a 7-day of incubation. The heavy portion of DNA(13C-DNA) was separated from the light portion of DNA (12C-DNA) using equilibrium density gradient ultracentrifuge. Bacterial community structure in the 13C-DNAsample was analyzed by t-RFLP (terminal restriction fragment length polymorphism) method. The t-RFLP result demonstates that the use of SIP efficiently and selectively enriched the genomes of biphenyl degrading bacteria from non-degradative microbes. Furthermore, the bacterial diversity of biphenyl degrading populations was small enough for environmental genomes tools (metagenomics and DNA microarrays) to be used to detect functional (biphenyl degradation) genes from soil microbial communities, which may provide a significant progress in assessing microbial capability of PCB bioremediation in soil and groundwater.

• 인터넷정보학회논문지
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• 제18권5호
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• pp.47-53
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• 2017

고처리 시퀀싱과 빅데이터 및 크라우드 컴퓨팅에 혁신이 일어나면서, RNA 시퀀싱도 획기적인 변화가 일어, RNAseq가 기존의 DNA 마이크로어레이를 대체하여, 빅-데이터를 형성하고 있다. 현재, RANseq 이용한 유전자 조절망(GRN) 까지 연구가 활성화 되고 있는데, 그 중 한 분야가 GRN의 기본 요소인 특징 유전자를 빅-데이터에서도 구별하고 기존에 알려진 것 외에 새로운 역할을 찾는 것이다. 그러나, 이러한 연구 방향에 부합하는 빅-데이터를 처리할 수 있는 컴퓨테이션 방법이 아직까지 매우 부족하다. 따라서 본 논문에서는 RNAseq 빅-데이터를 처리할 수 있도록 기존의 SVM-RFE알고리즘을 밀집도-의존 정규화에 병합하여, NCBI-GEO와 같은 빅-데이터에서 공개된 일부의 데이터에 개선된 알고리즘을 적용하고 해당 알고리즘에 의해 나온 결과의 성능을 평가한다.

• 방사선산업학회지
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• 제4권4호
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• pp.325-334
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• 2010

Transcriptional regulation in response to salt in mutant lines was investigated using oligonucleotide microarrays. In order to characterize the salt-responsive genes in rice, the expression profiles of transcripts that responded to salt-treatment were monitored using the microarrays. In the microarray analysis, among 37,299 reliable genes, 5,101, 2,758 and 2,277 genes were up-regulated by more than 2-fold using the salt treatment, while the numbers of down-regulated genes were 4,619, 3,234, and 1,878 in the WT, ST-495, and ST-532, respectively. From genotype changes induced by gamma ray mutagenesis, 3,345 and 2,397 genes were up-regulated, while 2,745 and 2,075 genes were down-regulated more than 2-fold in the two untreated mutants lines compared with untreated WT, respectively. A total of 3,108 and 2,731 genes were up-regulated more than 2-fold, while 3,987 and 3,660 genes were down-regulated by more than 2-fold in the salt treatment of the two mutants lines compared with the salt treated WT, respectively. The expressions of membrane transporter genes such as OsAKT1, OsKUP, and OsNAC increased more severely in ST-495 and ST-532 than in the WT. The expressions of the proline accumulation related genes such as OsP5CS and OsP5CR were also markedly increased in the salt tolerant mutants when compared to the WT plant.