• YAKHAK HOEJI
• /
• v.51 no.3
• /
• pp.179-185
• /
• 2007

Gastric cancer is one of the most common malignancies in Korea, but the predominant molecular event underlying gastric carcinogenesis remain unknown. Recently, DNA microarray technology has enabled the comprehensive analysis of gene expression level, and as such has yielded great insight into the molecular nature of cancer, However, despite the powerful approach of this techniques, the technical artifacts and/or bias in applied array platform limited the liability of resultant tens of thousand data points from microarray experiments. Therefore, we applied two different any platforms, such as olignucleotide microarray and cDNA microarray, to identify gastric cancer related large-scale molecular signature of the same human specimens. When thirty sets of matched human gastric cancer and normal tissues subjected to oligonucleotide microarray, total 623 genes were resulted as differently expressed genes in gastric cancer compared to normal tissues, and 252 genes for cDNA microarray analysis. In addition, forty three outlier genes which reflect the characteristic expression signature of gastric cancer beyond array platform and analytical protocol was recapitulated from two different expression profile. In conclusion, we were able to identify robust large-scale molecular changes in gastric cancer by applying two different platform of DNA microarray, this may facilitate to understand molecular carcinogenesis of gastric cancer.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2001.10a
• /
• pp.29-44
• /
• 2001

DNA damage by physical insult including UV and g-radiation might provoke genetic alterations in cells, which is followed by either acute cell death or tumorigenesis. The responsiveness to g-radiation depends on cellular context of target cells. To understand the mechanisms of checkpoint control, repair and cell death following genotoxic stimu]i, cDNA microarray can provide the gene expression profile. To make a profile of gene expression in irradiated Jurkat T cells, we hybridized the cDNA microarray using cDNA from g-irradiated Jurkat T cells. Jurkat T cells were exposed to 4Gy to 16Gy, and total RNA were extracted at 4 to 24 hrs after irradiation. The hybridization of the microarray to fluorescence-labeled cDNA from treated and untreated cells was analyzed by bioinformatic analysis to address relative changes in expression levels of the genes present in the array. Responses varied widely in different time points, suggesting acute stress response and chronic restoration or cell death. From these results we could select 384 genes related to radiation response in Tcells, and radiation response might be different in various types of cells. Using Radchip, we could separate "the exposed" from control PBMCs. We propose that Radchip might be useful to check the radiation research as well as radiation carcinogenesis.

• Proceedings of the Korean Statistical Society Conference
• /
• 2002.05a
• /
• pp.79-83
• /
• 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.

• Molecular & Cellular Toxicology
• /
• v.2 no.1
• /
• pp.35-47
• /
• 2006

2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin (TCDD) are well known as the most toxic environmental compound in these days. Many researches are reported that dioxin produces multiple toxic effects, such as endocrine toxicity, reproductive toxicity, immunotoxicity and cancer. In this study, we carried to discover novel evidence for previously unknown gene expression patterns in human exposed to dioxin by using radioactive cDNA microarray. 548 workers who were divided into experimental and control groups according to their urinary Naphthol levels were enrolled in our study. Blood mRNA in human was isolated, and the gene expression profiles were analyzed by cDNA microarray. Gene expression analysis identified 52 genes which exhibited a significant change. In our study, most notably, genes involved in cell cycle, cell proliferation, signal transduction and apoptosis in human exposed to dioxin, such as CCND3, TSHR, and EFRN5, were up-regulated. In the current study, we observed gene expression of people that are exposed to dioxin using radioactive cDNA microarray. Through these results, we suggest when objects are exposed to toxic compounds, such as dioxin, the radioactive cDNA microarray may be using in sensitively detecting of cancerous change.

• Genomics & Informatics
• /
• v.2 no.2
• /
• pp.92-98
• /
• 2004

A cDNA microarray experiment is one of the most useful high-throughput experiments in medical informatics for monitoring gene expression levels. Statistical analysis with a cDNA microarray medical data requires a normalization procedure to reduce the systematic errors that are impossible to control by the experimental conditions. Despite the variety of normalization methods, this. paper suggests a more general and synthetic normalization algorithm with a control gene set based on previous studies of normalization. Iterative normalization method was used to select and include a new control gene set among the whole genes iteratively at every step of the normalization calculation initiated with the housekeeping genes. The objective of this iterative normalization was to maintain the pattern of the original data and to keep the gene expression levels stable. Spatial plots, M&A (ratio and average values of the intensity) plots and box plots showed a convergence to zero of the mean across all genes graphically after applying our iterative normalization. The practicability of the algorithm was demonstrated by applying our method to the data for the human photo aging study.

• Journal of the Korean Data and Information Science Society
• /
• v.16 no.4
• /
• pp.951-958
• /
• 2005

As a foundation study of stem cell applied research, it is necessary to identify the large gene expression through cDNA microarray to understand principles of the level of molecular about cell function. In this paper, we investigated the gene expression through the K-means clustering method and path analysis with genes related to pluripoteny and differentiation in an mouse early stage embryonic development process and embryonic stem cell differentiation. We find a few biological phenomenon through this study. Also, we realize that this process provides functional relationship of unknown genes.

• Proceedings of the Korean Society of Sericultural Science Conference
• /
• 2003.04a
• /
• pp.47-48
• /
• 2003

The development of cDNA microarray has permitted the analysis of thousands of genes simultaneously. cDNA microarray has been used to analyze gene expression profiles during developmental stage in both single and multicellular organisms. Two significant factors contributing to the limitation of the development of cDNA microarray in the Bombyx mori are the shortage of accessible repositories of cDNA clones and ESTs and the relative scarcity of facilities to produce microarrays and analyze the data generated. (omitted)

• Asian-Australasian Journal of Animal Sciences
• /
• v.21 no.1
• /
• pp.11-18
• /
• 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.

• Pediatric Gastroenterology, Hepatology & Nutrition
• /
• v.8 no.2
• /
• pp.177-193
• /
• 2005

Purpose: To identify genes specifically expressed in biliary atresia, we compared the patterns of gene expression between biliary atresia and neonatal hepatitis syndrome using cDNA microarray analysis. Methods: Liver tissues were taken from livers of 11 patients (7 patients with biliary atresia and four with neonatal hepatitis) with neonatal cholestasis by needle biopsy. Normal control could be obtained from donor liver tissue during living-related liver transplantation. Total RNA was extracted from each samples and reversely transcribed to make cDNA. Then fluorescent cDNA were pooled and hybridized to the clones on the microarray. Fluorescence intensities at the immobilized targets were measured. Utilizing cDNA arrays of 4.7 K human genes, gene expression profiles were analyzed. Results: Among 4,700 microarray clones, 17 cDNA clones were significantly over-expressed in all 11 patients with neonatal cholestasis, while 20 clones were significantly decreased. Genome-wide expression analysis was carried out in livers obtained at the time of diagnosis. We could identify 49 genes, in which there showed differential expression between biliary atresia and neonatal hepatitis syndrome. Conclusion: This study shows the pattern of differentially expressed genes in biliary atresia and neonatal hepatitis syndrome. We believe that this study can contribute to the understanding of pathogenesis of neonatal cholestasis.

• Journal of Acupuncture Research
• /
• v.20 no.3
• /
• pp.34-44
• /
• 2003

Objective : Bone homeostasis is maintained by balance of bone formation and resorption. Therefore, bone related diseases arose by disturbance of this balance between osteoblast and osteoclast activities. To develop a successful screening system the therapeutic components based on oriental medicine is essential to set up systematic approach for that purpose. The purpose of this study is to the know the gene expression using cDNA microarray assay. Methods : Cervi Pantotricuhum Cornu Herbal-acupuncture extract was prepared by boiling. human osteosarcoma cells(HOS) were treated with Cervi Pantotricuhum Cornu Herbal-acupuncture solution. Then mRNA was extracted and cDNA microarray assay was performed. Results : Human osteosarcoma cells(HOS) treated with Cervi Pantotricuhum Cornu Herbal-acupuncture solution($500{\mu}g/m{\ell}$) showed that thioredoxin, TAFII31 and two novel genes were increased. However many genes decreased their expression by Cervi Pantotricuhum Cornu Herbal-acupuncture. Conclusions : This type of approach will give a good chance to explore the favorable effects of Cervi Pantotricuhum Cornu Herbal-acupuncture. Further study is needed for investigating the effect of Cervi Pantotricuhum Cornu Herbal-acupuncture.