• Genomics & Informatics
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• v.8 no.1
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• pp.34-40
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• 2010

Radiofrequency (RF) radiation might induce the transcription of a certain set of genes as other physical stresses like ionizing radiation and UV. To observe transcriptional changes upon RF radiation, we exposed WI-38, human lung fibroblast cell to 1763 MHz of mobile phone RF radiation at 60 W/kg of specific absorption rate (SAR) for 24h with or without heat control. There were no significant changes in cell numbers and morphology after exposure to RF radiation. Using quantitative RT-PCR, we checked the expression of three heat shock protein (HSP) (HSPA1A, HSPA6 and HSP105) and seven stress-related genes (TNFRSF11B, FGF2, TGFB2, ITGA2, BRIP1, EXO1, and MCM10) in RF only and RF/HS groups of RF-exposed cells. The expressions of three heat shock proteins and seven stress-related genes were selectively changed only in RF/HS groups. Based on the expression of ten genes, we could classify thermal and non-thermal effect of RF-exposure, which genes can be used as biomarkers for RF radiation exposure.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3763-3766
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• 2014

Human mammary epithelial cells have different proliferative statuses and demonstrate a close relationship with age and cell proliferation. Research on this topic could help understand the occurrence, progression and prognosis of breast cancer. In this article, using significance analysis of a microarray algorithm, we analyzed gene expression profiles of human mammary epithelial cells of different proliferative statuses and different age groups. The results showed there were significant differences in gene expression in the same proliferation status between elderly and young groups. Three common differentially expressed genes were found to dynamically change with the proliferation status and to be closely related to tumorigenesis. We also found elderly group had less status-related differential genes from actively proliferating status to intermediate status and more statusrelated differential genes from intermediate status than the young group. Finally, functional enrichment analyses allowed evaluation of the detailed roles of these differentially-expressed genes in tumor progression.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2003.10a
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• pp.176-176
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• 2003

Methylmercury is known to have devastating effects on the mammalian nervous system. When human neuroblastoma SH-SY5Y cells were treated with methylmercury at sublethal concentrations (6.25 uM), up-regulated genes (39) ＆ down-regulated genes (19) were identified by human 8k cDNA microarray. These genes are related with microtubule process, signal transduction pathway and cell death (apoptosis), Apoptosis-associated genes, HSP70, CDK inhibitor 1, FOS-like antigen were up-regulated and microtubule related genes like villin and dynein down-regultaed. To confirm the presence of apoptosis in cultured SH-SY5Y cells treated 6.25 and 1 uM methylmercury, we applied Annexin V-FITC assay followed by flow cytometric measurements after 6 and 24h. Studies on transcriptional and molecular effect by methylmercury may provide an insight into the neurotoxic effects of methylmercury in human neuronal cells and a possibility to develop more efficient and exact monitoring system of heavy metals as ubiquitous environmental pollutants.

• Toxicological Research
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• v.20 no.2
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• pp.109-116
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• 2004

For the safety evaluation of adenovirus-mediated gene transfer, we investigated differential gene expressions after transfecting adenoviral vector containing p16 tumor suppressor gene (Ad5CMV-p16) into human non-small cell lung cancer cells. In the previous study, we showed adenovirus-mediated $p16^{INK4a}$ gene transfer resulted in significant inhibition of cancer cell growth. We investigated gene expression changes after transfecting Ad5CMV-p16, Ad5CMV (null type, a mock vector) into A549 cells by using cDNA chip and oligonucleotide microarray chip (1200 genes) which carries genes related with signal transduction pathways, cell cycle regulations, oncogenes and tumor suppressor genes. We found that $p16^{INK4a}$ gene transfer down regulated 5 genes (cdc2, cyclin D3, cyclin B, cyclin E, cdk2) among 26 genes involved in cell cycle regulations. Compared with serum-free medium treated cells, Ad5CMV-p16 changed 27 gene expressions, two fold or more on oligonucleotide chip. In addition, Ad5CMV-p16 did not seem to increase the tumorigenicity-related gene expression in A549 cells. Further studies will be needed to investigate the effect of Ad5CMV-p16 on normal human cells and tissues for safety evaluation.

• Journal of Physiology & Pathology in Korean Medicine
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• v.19 no.6
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• pp.1534-1540
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• 2005

In order to testify the urate lowering effects of Daihwangmudan-tang(DMT), ICR mice were injected monosodium urate into the abdominal cavity and then DMT was administered on 2 and 4 days after Injection. Uric acid and triglyceride were measured as hematological indices of gout, and some genes related with this change were identified by ACP based GeneFishing PCR method and direct sequencing. From this experiment, DMT highly decreased the blood levels of uric acid and significantly suppressed and lowered the acute increment of triglyceride level. There were 11 differentially expressed genes(DEG) having relations with positive actions of DMT, and 4 major genes in the middle of DEGs were sequenced; Mfap 2, jagged 2, Hsd17b7, DkkI-1, These genes were supposed that several mechanisms through interleukin 1 and T-cell anergy, LDL cholesterol metabolism, wnt pathway would be related with the anti-inflammation effect against gout.

• The Korean Journal of Food And Nutrition
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• v.15 no.3
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• pp.191-196
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• 2002

The effect of allicin, the major component of garlic (Allium sativum), on the gene expression profiles of peripheral blood mononuclear cells from healthy donors was analyzed. DNA microarray which can detect expression signal of 862 genes revealed that allicin induced the expression of cytokine, chemokine, and immune-related genes in peripheral blood mononuclear cells. In contrast, allicin repressed the expression of adaptive immune-related genes, which are expressed in T helper 1 Iymphocytes. Simultaneous inhibitory and stimulatory effects of allicin were found on inflammatory cells. It is likely that allicin down-regulated the expression of specific genes that were previously up-regulated in resting cells, suggesting a new mechanism by which they exert positive and negative effect. Considering the broad and renewed interest in allicin, the profiles we describe here will be useful in designing more specific and efficient treatment strategies.

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.12 no.2
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• pp.167-172
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• 2012

In biology the advent of the high-throughput technology for sequencing, probing, or screening has produced huge volume of data which could not be manually handled. Biologists have resorted to software tools in order to effectively handle them. This paper introduces a bioinformatics tool to help biologists find potentially interesting pathway maps from a transcriptome data set in which the expression levels of genes are described for both case and control samples. The tool accepts a transcriptome data set, and then selects and categorizes some of genes into four classes using a fuzzy filtering technique where classes are defined by membership functions. It collects and edits the pathway maps related to those selected genes without analyst' intervention. It invokes a sequence of web service functions from KEGG, which an online pathway database system, in order to retrieve related information, locate pathway maps, and manipulate them. It maintains all retrieved pathway maps in a local database and presents them to the analysts with graphical user interface. The tool has been successfully used in identifying target genes for further analysis in transcriptome study of human cytomegalovirous. The tool is very helpful in that it can considerably save analysts' time and efforts by collecting and presenting the pathway maps that contain some interesting genes, once a transcriptome data set is just given.

• The Plant Pathology Journal
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• v.35 no.5
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• pp.530-537
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• 2019

Fuji, a major apple cultivar in Korea, is susceptible to white rot. Apple white rot disease appears on the stem and fruit; the development of which deteriorates fruit quality, resulting in decreases in farmers' income. Thus, it is necessary to characterize molecular markers related to apple white rot resistance. In this study, we screened for differentially expressed genes between uninfected apple fruits and those infected with Botryosphaeria dothidea, the fungal pathogen that causes white rot. Antimicrobial tests suggest that a gene expression involved in the synthesis of the substance inhibiting the growth of B. dothidea in apples was induced by pathogen infection. We identified seven transcripts induced by the infection. The seven transcripts were homologous to genes encoding a flavonoid glucosyltransferase, a metallothionein-like protein, a senescence-induced protein, a chitinase, a wound-induced protein, and proteins of unknown function. These genes have functions related to responses to environmental stresses, including pathogen infections. Our results can be useful for the development of molecular markers for early detection of the disease or for use in breeding white rotresistant cultivars.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.253-253
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• 2022

Codonopsis lanceolata (C. lanceolata) has been widely used in East Asia as a traditional medicine to treat various diseases such as bronchitis, convulsions, cough, obesity, and hepatitis. C. lanceolata belonging to Campanulaceae contains bioactive compounds such as polyphenols, saponins, and steroids. However, despite the pharmacological significance of C. lanceolata, the genetic information of this plant is limited and there are few studies of its transcriptome. In this study, we constructed a unigene set of C. lanceolata using Pac-Bio sequencing. Furthermore, the reads generated from Pac-bio and Illumina sequencing were mixed and assembled using rnaSPAdes. All genes involved in the triterpenoid pathway, a major bioactive compounds of C. lanceolata, were searched from the two unigene sets and the expression profiles of these genes were analyzed. The results showed that lupeol, beta-amyrin, and dammarenediol synthesis genes were activated in the leaves and roots of C. lanceolata. In particular, the expression of genes related to lupeol synthesis was relatively high, suggesting that the main triterpenoid of C. lanceolata is lupeol. Transcriptome studies related to lupeol synthesis in C. lanceolata have been rarely reported. Lupeol has been reported to have pharmacological effects such as anti-inflammatory, anti-cancer, and anti-bacterial. This study suggests the importance of C. lanceolata as a lupeol producing plant.

• Genomics & Informatics
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• v.10 no.1
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• pp.33-39
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• 2012

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.