• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.871-884
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• 2009

Gene expression profiling is a useful tool for identifying critical genes and pathways in metabolism. The objective of this study was to determine the major differences in the expression of genes associated with metabolism and metabolic regulation in liver and mammary tissues of lactating cows. We used the Michigan State University bovine metabolism (BMET) microarray; previously, we have designed a bovine metabolism-focused microarray containing known genes of metabolic interest using publicly available genomic internet database resources. This is a high-density array of 70mer oligonucleotides representing 2,349 bovine genes. The expression of 922 genes was different at p<0.05, and 398 genes (17%) were differentially expressed by two-fold or more with 222 higher in liver and 176 higher in mammary tissue. Gene ontology categories with a high percentage of genes more highly expressed in liver than mammary tissues included carbohydrate metabolism (glycolysis, glucoenogenesis, propanoate metabolism, butanoate metabolism, electron carrier and donor activity), lipid metabolism (fatty acid oxidation, chylomicron/lipid transport, bile acid metabolism, cholesterol metabolism, steroid metabolism, ketone body formation), and amino acid/nitrogen metabolism (amino acid biosynthetic process, amino acid catabolic process, urea cycle, and glutathione metabolic process). Categories with more genes highly expressed in mammary than liver tissue included amino acid and sugar transporters and MAPK, Wnt, and JAK-STAT signaling pathways. Real-time PCR analysis showed consistent results with those of microarray analysis for all 12 genes tested. In conclusion, microarray analyses clearly identified differential gene expression profiles between hepatic and mammary tissues that are consistent with the differences in metabolism of these two tissues. This study enables understanding of the molecular basis of metabolic adaptation of the liver and mammary gland during lactation in bovine species.

• Journal of fish pathology
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• v.36 no.2
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• pp.191-211
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• 2023

Rock bream iridovirus (RBIV) causes high mortality and economic losses in rock bream (Oplegnathus fasciatus) aquaculture industry in Korea. Although, the immune responses of rock bream under RBIV infection have been studied, there is not much information at the different stages of infection (initial, middle and recovery). Gene expression profiling of rock bream under different RBIV infection stages was investigated using a microarray approaches. In total, 5699 and 6557 genes were significantly up- or down-regulated over 2-fold, respectively, upon RBIV infection. These genes were grouped into categories such as innate immune responses, adaptive immune responses, complements, lectin, antibacterial molecule, stress responses, DNA/RNA binding, energy metabolism, transport and cell cycle. Interestingly, hemoglobins (α and β) appears to be important during pathogenesis; it is highly up-regulated at the initial stage and is gradually decreased when the pathogen most likely multiplying and fish begin to die at the middle or later stage. Expression levels were re-elevated at the recovery stage of infection. Among up-regulated genes, interferon-related genes were found to be responsive in most stages of RBIV infection. Moreover, X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) expression was high, whereas expression of apoptosis-relate genes were low. In addition, stress responses were highly induced in the virus infection. The cDNA microarray data were validated using quantative real-time PCR. Our results provide novel inslights into the broad immune responses triggered by RBIV at different infection stages.

• The Journal of the Korean Society for Microbiology
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• v.35 no.4
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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.

• The Korean Journal of Applied Statistics
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• v.26 no.3
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• pp.389-399
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• 2013

This article introduces Gaussian process regression and shows its application with time-course microarray gene expression data. Gene screening for yeast cell cycle microarray expression data is accomplished with a ratio of log marginal likelihood that uses Gaussian process regression with a squared exponential covariance kernel function. Gaussian process regression fitting with each gene is done and shown with the nine top ranking genes. With the screened data the Gaussian model-based clustering is done and its silhouette values are calculated for cluster validity.

• The Journal of Korean Medicine
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• v.24 no.2
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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.

• Journal of Environmental Science International
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• v.24 no.5
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• pp.623-631
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• 2015

Microarray technology provides a unique tool for the determination of gene expression at the level of messenger RNA (mRNA). This study, the mRNA expression profiles provide insight into the mechanism of action of cadmium in Fleshy shrimp (Fenneropenaeus chinensis). The ability of genomic technologies was contributed decisively to development of new molecular biomarkers and to the determination of new possible gene targets. Also, it can be approach for monitoring of trace metal using oligo-chip microarray-based in potential model marine user level organisms. 15K oligo-chip for F. chinensis that include mostly unique sets of genes from cDNA sequences was developed. A total of 13,971 spots (1,181 mRNAs up- regulated and 996 down regulated) were identified to be significantly expressed on microarray by hierarchical clustering of genes after exposure to cadmium for different conditions (Cd24-5000 and Cd48-1000). Most of the changes of mRNA expression were observed at the long time and low concentration exposure of Cd48-1000. But, gene ontology analysis (GO annotation) were no significant different between experiments groups. It was observed that mRNA expression of main genes involved in metabolism, cell component, molecular binding and catalytic function. It was suggested that cadmium inhibited metabolism and growth of F. chinensis.

• Journal of Periodontal and Implant Science
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• v.34 no.1
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• pp.205-221
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• 2004

Periodontal ligament(PDL) cells have been known as playing an important roles in periodontal regeneration and gingival fibroblasts are also important to periodontal regeneration by forming connective tissue attachment. There were rare studies about the gene expression patterns of PDL cells and gingival fibroblasts, therefore in this study, we tried cDNA microarray-based gene expression monitoring to explain the functional differences of PDL cells and gingival fibroblasts in vivo and to confirm the characteristics of PDL cells. Total RNA were extracted from PDL cells and gingival fibroblasts of same person and same passages, and mRNA were isolated from the total RNA using Oligotex mRNA midi kit(Qiagen) and then fluorescent cDNA probe were prepared. And microarray hybridization were performed. The gene expression patterns of PDL cells and gingival fibroblasts were quite different. About 400 genes were expressed more highly in the PDL cells than gingival fibroblasts and about 300 genes were more highly expressed in the gingival fibroblasts than PDL cells. Compared growth factor- and growth factor receptor-related gene expression patterns of PDL cells with gingival fibroblasts, IGF-2, IGF-2 associated protein, nerve growth factor, placental bone morphogenic protein, neuron-specific growth- associated protein, FGF receptor, EGF receptor-related gene and PDGF receptor were more highly expressed in the PDL cells than gingival fibroblasts. The results of collagen gene expression patterns showed that collagen type I, type III, type VI and type VII were more highly expressed in the PDL cells than gingival fibroblasts, and in the gingival fibroblasts collagen type V, XII were more highly expressed than PDL cells. The results of osteoblast-related gene expression patterns showed that osteoblast specific cysteine-rich protein were more highly expressed in the PDL cells than gingival fibroblasts. The results of cytoskeletal proteins gene expression patterns showed that a-smooth muscle actin, actin binding protein, smooth muscle myosin heavy chain homolog and myosin light chain were more highly expressed in the PDL cells than gingival fibrobalsts, and ${\beta}-actin$, actin-capping protein(${\beta}$ subunit), actin- related protein Arp3(ARP) and myosin class I(myh-1c) were more highly expressed in the gingival fibroblasts than PDL cells. Osteoprotegerin/osteoclastogenesis inhibitory factor(OPG/OCIF) was more highly expressed in the PDL cells than gingival fibroblasts. According to the results of this study, PDL cells and gingival fibroblasts were quite different gene expression patterns though they are the fibroblast which have similar shape. Therefore PDL cells & gingival fibroblasts are heterogeneous populations which represent distinct characteristics. If more studies about genes that were differently expressed in each PDL cells & gingival fibroblasts would be performed in the future, it would be expected that the characteristics of PDL cells would be more clear.

• Proceedings of the Korean Statistical Society Conference
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• 2002.05a
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• pp.85-90
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• 2002

Microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. In time-course experiments in which gene expression is monitored over time we are interested in testing gene expression profiles for different experimental groups. We propose a statistical test based on the ANOVA model to identify genes that have different gene expression profiles among experimental groups in time-course experiments. Using this test, we can detect genes that have different gene expression profiles among experimental groups. The proposed model is illustrated using cDNA microarrays of 3,840 genes obtained in an experiment to search for changes in gene expression profiles during neuronal differentiation of cortical stem cells.

• Communications for Statistical Applications and Methods
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• v.12 no.2
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• pp.335-348
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• 2005

The rapid development of microarray technologies enabled the monitoring of expression levels of thousands of genes simultaneously. Recently, the time course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. For the data, biologists are attempting to group genes based on the temporal pattern of their expression levels. We apply the consensus clustering algorithm to a time course gene expression data in order to infer statistically meaningful information from the measurements. We evaluate each of consensus clustering and existing clustering methods with various validation measures. In this paper, we consider hierarchical clustering and Diana of existing methods, and consensus clustering with hierarchical clustering, Diana and mixed hierachical and Diana methods and evaluate their performances on a real micro array data set and two simulated data sets.

• Journal of Nutrition and Health
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• v.35 no.10
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• pp.1053-1059
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• 2002

In post-genome period, the technique for identifying gene expression has been changed to high throughput screening. In the field of molecular nutrition, the need for this technique to clarify molecular function of the specific nutrient is essential. In this study, we have tested the zinc-regulated gene expression in zinc-deficient U937 cells, using cDNA microarray which is the cutting-edge technique to screen large numbers of gene expression simultaneously. The study result can be used for the preliminary gene screening data for clarifying, using monocyte U937 cell line, molecular Zn aspect in atherosclerosis. U937 cells were cultured in Zn-adequate (control, 12 $\mu$M Zn) or Zn-deficient (experimental, 0 $\mu$M Zn) ESMI media during 2 days, respectively. Cells were harvested and RNA was extracted. Total RNA was reverse-transcriptinized and synthesized cDNA probe labeled with Cy-3. fluorescent labeled cDNA probe was applied to microarray slide for hybridization slide, and after then, the slide was scanned using fluorescence scanner. ‘Highly expressed genes’ in Zn-deficient U937 cells, comparing to Zn-adequate group, are mainly about the genes for motility protein, immune system protein, oncogene and tumor suppressor and ‘Less highly expressed genes’ are about the genes for transcription, apoptosis associated protein, cell cycle, and several basic transcription factors. The results of this preliminary study imply the effectiveness of cDNA microarray for expression profiling of a singly nutrient deficiency, specially Zn. Furthur study, using tailored-cDNA array and capillary endothelial cell lines, would be beneficial to clarify molecular Zn function, more in detail.