• The Korean Journal of Physiology and Pharmacology
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• 제15권1호
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• pp.23-29
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• 2011

Melatonin, which is the main product of the pineal gland, has well documented antioxidant and immune-modulatory effects. Macrophages produce molecules that are known to play roles in inflammatory responses. We conducted microarray analysis to evaluate the global gene expression profiles in response to treatment with melatonin in lipopolysaccharide (LPS) activated RAW 264.7 macrophage cells. In addition, eight genes were subjected to real-time reverse transcription polymerase chain reaction (RT-PCR) to confirm the results of the microarray. The cells were treated with LPS or melatonin plus LPS for 24 hr. LPS induced the up-regulation of 1073 genes and the down-regulation of 1144 genes when compared to the control group. Melatonin pretreatment of LPS-stimulated RAW 264.7 cells resulted in the down regulation of 241 genes and up regulation of 164 genes. Interestingly, among genes related to macrophage-mediated immunity, LPS increased the expression of seven genes (Adora2b, Fcgr2b, Cish, Cxcl10, Clec4n, Il1a, and Il1b) and decreased the expression of one gene (Clec4a3). These changes in expression were attenuated by melatonin. Furthermore, the results of real-time PCR were similar to those of the microarray. Taken together, these results suggest that melatonin may have a suppressive effect on LPS-induced expression of genes involved in the regulation of immunity and defense in RAW 264.7 macrophage cells. Moreover, these results may explain beneficial effects of melatonin in the treatment of various inflammatory conditions.

• Asian-Australasian Journal of Animal Sciences
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• 제21권1호
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• pp.11-18
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• 2008

We created a cDNA microarray representing approximately 3,500 pig genes for functional genomic studies. The array elements were selected from 6,494 cDNA clones identified in a large-scale expressed sequence tag (EST) project. These cDNA clones came from normalized and subtracted porcine adipose tissue cDNA libraries. Sequence similarity searches of the 3,426 ESTs represented on the array using BLASTN identified 2,790 (81.4%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. We used the gene microarray to profile transcripts expressed by adipose tissue of fatty Chinese Xiang pig (XP) and muscley Large White (LW). Microarray analysis of RNA extracted from adipose tissue of fatty XP and muscley LW identified 81 genes that were differently expressed two fold or more. Transcriptional differences of four of these genes, adipocyte fatty acid binding protein (aP2), stearyl-CoA desaturase (SCD), sterol regulatory element binding transcription factor 1 (SREBF1) and lipoprotein lipase (LPL) were confirmed using SYBR Green quantitative RT-PCR technology. Our results showed that high expression of SCD and SREBF1 may be one of the reasons that larger fat deposits are observed in the XP. In addition, our findings also illustrate the potential power of microarrays for understanding the molecular mechanisms of porcine development, disease resistance, nutrition, fertility and production traits.

• Korean Journal of Acupuncture
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• 제23권2호
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• pp.125-136
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• 2006

Objectives: It has long been known about the osteogenic effect of CPC-HAS(cervi parvum cornu herbal-acupuncture solution) on bone tissues. However, it has not been determined the effect of CPC-HAS on cancer cells. The purpose of this study is to screen the CPC-HAS mediated differentially expressed genes..in cancer cells such as SNU484 gastric cancer cell lines. Oligonucleotide microarray approache was employed to screen the differential expression genes. Methods: CPC-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of CPC-HAS (0.1, 0.5, 1.5, 10, 20 mg/ml) for 24 h. Cell toxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with 1.5 mg/ml of CPC-HAS. For oligonucleotide microarray assay, total RNA was used for gene expression analysis using oligonucleotide Genechip(Human genome U133 Plus 2.0., Affimatrix Co.). Results: It has no cytotoxic effects on SNU484 cell in all concentrations(0.l, 0.5, 1.5, 10, 20 mg/ml). In oligonucleotide microarray assay, in SNU484 cells, the number of more than twofold up-regulated genes was 5 while, the number of more than twofold down-regulated genes was 10. Conclusions: This study showed the screening of CPC-HAS mediated differentially regulated genes using combined approaches of oligonucleotide microarray. The screened genes will be used for the better understanding of the therapeutic effects of CPC-HAS on cancer fields.

• Journal of the Korean Data and Information Science Society
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• 제23권1호
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• pp.39-51
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• 2012

군집분석은 마이크로어레이 발현자료에서 유전자 혹은 표본들의 유사한 특성을 갖는 연관구조를 조사하는데 중요한 도구이다. 본 논문에서는 마이크로어레이 자료에서 계층적 군집방법, K-평균법, PAM (partitioning around medoids), SOM (self-organizing maps) 그리고 모형기반 군집방법 들의 성능을 3가지 군집 타당성 측도인 내적 측도, 안정적 측도 그리고 생물학적 측도를 가지고 비교분석하고자 한다. 모의실험을 통해 생성된 자료와 실제 SRBCT (small round blue cell tumor) 자료를 가지고 여러 가지 군집방법들의 성능을 비교하였으며 그 결과 모의실험 자료에서는 거의 모든 방법들이 3가지 군집측도에서 원래 자료와 일치하는 좋은 군집 결과를 나타내었고 SRBCT 자료에서는 모의실험 자료처럼 명확한 군집화 결과를 보여주지는 않으나 내적측도의 실루엣 너비 (Silhouette width) 관점에서는 PAM 방법, SOM, 모형기반 군집방법 그리고 생물학적 측도에서는 PAM 방법과 모형기반 군집방법이 모의실험 결과와 비슷한 결과를 얻었고 안정적 측도에서 모형기반 군집방법이 다른 방법들보다 좋은 군집결과를 보여주었다.

• 한국정보통신학회논문지
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• 제15권3호
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• pp.747-752
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• 2011

마이크로어레이 분류는 전형적으로 분류기 디자인과 에러 추정이 현저하게 작은 샘플에 기반한다는 것과 교차 검증 에러 추정이 대다수의 논문에 사용된다는 주목할 만한 두 가지 특징을 소유한다. 마이크로어레이 난소 암 데이터는 수 만개의 유전자 발현으로 구성되어 있고, 이러한 정보를 동시에 분석하기 위한 어떤 체계적인 절차도 없다. 본 논문에서는, 통계에 따라 유전자의 우선순위를 정함으로써 표지유전자를 선택하였고, 널리 보급되어 있는 분류 규칙인 선형 분류 분석, 3-nearest-neighbor와 결정 트리 알고리즘은 표지 유전자를 선택한 데이터와 선택하지 않는 데이터의 분류 정확도 비교를 위해 사용되어졌다. ANOVA를 이용하여 선택된 표지 유전자를 포함하는 마이크로어레이 데이터 셋에 선영 분류분석 규칙을 적용한 결과 97.78%의 가장 높은 분류 정확도와 가장 낮은 예측 에러 추정치를 나타내었다.

• Genomics & Informatics
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• 제4권3호
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• pp.97-102
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• 2006

In acute leukemia patients, several successful methods of expression profiling have been used for various purposes, i.e., to identify new disease class, to select a therapeutic target, or to predict chemo-sensitivity and clinical outcome. In the present study, we tested the peripheral blood of 47 acute leukemia patients in an attempt to identify differentially expressed genes in AML and ALL using a Korean-made 10K oligo-nucleotide microarray. Methods: Total RNA was prepared from peripheral blood and amplified for microarray experimentation. SAM (significant analysis of microarray) and PAM (prediction analysis of microarray) were used to select significant genes. The selected genes were tested for in a test group, independently of the training group. Results: We identified 345 differentially expressed genes that differentiated AML and ALL patients (FWER<0.05). Genes were selected using the training group (n=35) and tested for in the test group (n=12). Both training group and test group discriminated AML and ALL patients accurately. Genes that showed relatively high expression in AML patients were deoxynucleotidyl transferase, pre-B lymphocyte gene 3, B-cell linker, CD9 antigen, lymphoid enhancer-binding factor 1, CD79B antigen, and early B-cell factor. Genes highly expressed in ALL patients were annexin A 1, amyloid beta (A4) precursor protein, amyloid beta (A4) precursor-like protein 2, cathepsin C, lysozyme (renal amyloidosis), myeloperoxidase, and hematopoietic prostaglandin D2 synthase. Conclusion: This study provided genome wide molecular signatures of Korean acute leukemia patients, which clearly identify AML and ALL. Given with other reported signatures, these molecular signatures provide a means of achieving a molecular diagnosis in Korean acute leukemia patents.

• 대한약침학회지
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• 제9권2호
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• pp.39-47
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• 2006

Objective : It has long been known about the anticancer effect of GRR-HAS, however, it has not been systemically determined the differentially regulated genes by GRR-HAS in cancer cells. The purpose of this study is to screen the GRR-HAS mediated differentially expressed genes in cancer cells such as SNU484 gastric cancer cell lines. Oligonucleotide microarray approache was employed to screen the differential expression genes. Methods : GRR-HAS was prepared by boiling and stored at $-70^{\circ}C$ until use. Cells were treated with various concentrations of GRR-HAS(0.1, 0.5, 1.5, 10, 20mg/ml) for 24 h. Cell toxicity was tested by MTT assay. To screen the differentially expressed genes in cancer cells, cells were treated with 1.5mg/ml of GRR-HAS. For oligonucleotide microarray assay, total RNA was used for gene expression analysis using oligonucleotide Genechip (Human genome Ul33 Plus 2.0., Affimatrix Co.). Results : It has no cytotoxic effects on both HepG2 and SNU484 cells in all concentrations(0.1, 0.5, 1.5, 10, 20mg/ml). In oligonucleotide microarray assay, in SNU484 cells, the number of more than twofold up-regulated genes was 346. The number of more than twofold down-regulated genes was 9. Discussion : This study showed the comprehensive gene expression analysis using oligonucleotide microarray for the screening of GRR-HAS mediated differentially regulated genes. These results will provide a better application of GRR-HAS in cancer field and drug target development.

• 환경생물
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• 제22권3호
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• pp.472-477
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• 2004

본 연구에서는 감마선으로 유도된 돌연변이체들에서 공통으로 발현되는 방사선 관련 유전자들의 발현을 연구하기 위하여, B. lentimorbus WJ5 의 방사선 유도 돌연변이체에서 발현되는 유전자를 DNA microarray로 동시에 탐색하였다. DNA microarray는 B. lentimorbus WJ5 genome을 무작위로 절단하여 2,000 단편으로 구성하였으며, 감마선 $(^{60}/Co)$으로 유도된 7 돌연변이체의 발현을 정량적으로 관찰하였다. 클러스터 분석결과 발현된 408 유전자 중 27개가 감마선 유도 돌연변이체 모두에서 유의하게 발현이 증가되었다. 특히, 복구(mutL, mutM) 에너지 대사 (acsA, sdhB, pgk, yhjB, citB), protease (npr), 산화자극에 대한 환원 (HMM)관련 유전자들이 동시에 증가되었다. 이는 감마선 유도 돌연변이체들에서 자발적인 직/간접 복구 관련 유전자의 발현 증가는 방사선 노출 직후 보이는 stress response와는 다른 현상임을 나타내는 것으로 생각된다.

• 한국작물학회지
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• 제54권3호
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• pp.332-338
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• 2009

Rapid extension of genomic database leads to the remarkable advance of functional genomics. This study proposes a novel methodology of functional analysis using 5-methyltrytophan (5 MT) mutant together with their 2-DE analysis and public microarray database. A total of 24 proteins was changed in 5 MT mutant and four remarkably different expressed proteins were identified. Among them, three spots were converted to Affymetrix probe. A total of 155 microarray samples from Gene Expression Omnibus (GEO) in NCBI was retrieved and followed by constructing gene co-expression networks over a broad range of biological issues through Self-Organising Tree Algorithm. Three co-expressing gene clusters were retrieved and each functional categorization with differential expression pattern was exhibited from 5 MT resistance mutant rice. It was indicated new co-expression networks in the mutant. This study suggests that on investigating possibility which correspond 2-DE to microarray database with their full potential.

• Asian-Australasian Journal of Animal Sciences
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• 제29권7호
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• pp.1044-1051
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• 2016

The present study compared the differential functions of two groups of adjuvants, Montanide incomplete Seppic adjuvant (ISA) series and Quil A, cholesterol, dimethyl dioctadecyl ammonium bromide, and Carbopol (QCDC) formulations, in chicken by analyzing published microarray data associated with each type of vaccine adjuvants. In the biological function analysis for differentially expressed genes altered by two different adjuvant groups, ISA series and QCDC formulations showed differential effects when chickens were immunized with a recombinant immunogenic protein of Eimeria. Among the biological functions, six categories were modified in both adjuvant types. However, with respect to "Response to stimulus", no biological process was modified by the two adjuvant groups at the same time. The QCDC adjuvants showed effects on the biological processes (BPs) including the innate immune response and the immune response to the external stimulus such as toxin and bacterium, while the ISA adjuvants modified the BPs to regulate cell movement and the response to stress. In pathway analysis, ISA adjuvants altered the genes involved in the functions related with cell junctions and the elimination of exogenous and endogenous macromolecules. The analysis in the present study could contribute to the development of precise adjuvants based on molecular signatures related with their immunological functions.