• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.107-116
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• 2004

The advent of microarray technologies gives an opportunity to moni tor the expression of ten thousands of genes, simultaneously. Such microarray data can be deteriorated by experimental errors and image artifacts, which generate non-negligible outliers that are estimated by 15% of typical microarray data. Thus, it is an important issue to detect and correct the se faulty probes prior to high-level data analysis such as classification or clustering. In this paper, we propose a systematic procedure for the detection of faulty probes and its proper correction in Genechip array based on multivariate statistical approaches. Principal component analysis (PCA), one of the most widely used multivariate statistical approaches, has been applied to construct a statistical correlation model with 20 pairs of probes for each gene. And, the faulty probes are identified by inspecting the squared prediction error (SPE) of each probe from the PCA model. Then, the outlying probes are reconstructed by the iterative optimization approach minimizing SPE. We used the public data presented from the gene chip project of human fibroblast cell. Through the application study, the proposed approach showed good performance for probe correction without removing faulty probes, which may be desirable in the viewpoint of the maximum use of data information.

• Molecular & Cellular Toxicology
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• v.3 no.2
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• pp.137-144
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• 2007

The mechanism of cytotoxicity of doxifluridine, a prodrug fluorouracil (5-FU), has been ascribed to the misincorporation of fluoropyrimidine into RNA and DNA and to the inhibition of the nucleotide synthetic enzyme thymidylate synthase. Increased understanding of the mechanism of 5-FU has led to the development of strategies that increases its anticancer activity or predicts its sensitivity to patients. Using GeneChip?? Rhesus Macaque Genome arrays, we analyzed gene expression profiles of doxifluridine after two weeks repeated administration in cynomolgus monkey. Kegg pathway analysis suggested that cytoskeletal rearrangement and cell adhesion remodeling were commonly occurred in colon, jejunum, and liver. However, expression of genes encoding extracellular matrix was distinguished colon from others. In colon, COL6A2, COL18A1, ELN, and LAMA5 were over-expressed. In contrast, genes included in same category were down-regulated in jejunum and liver. Interestingly, MMP7 and TIMP1, the key enzymes responsible for ECM regulation, were overexpressed in colon. Several studies were reported that both gene reduced cell sensitivity to chemotherapy-induced apoptosis. Therefore, we suggest they have potential as target for modulation of 5-FU action. In addition, the expression of genes which have been previously known to involve in 5-FU pathway, were examined in three organs. Particularly, there were more remarkable changes in colon than in others. In colon, ECGF1, DYPD, TYMS, DHFR, FPGS, DUT, BCL2, BAX, and BAK1 except CAD were expressed in the direction that was good response to doxifluridine. These results may provide that colon is a prominent target of doxifluridine and transcriptional profiling is useful to find new targets affecting the response to the drug.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.8
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• pp.1091-1101
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• 2009

In an attempt to understand the biochemical mechanism for the synthesis of the anabolic steroid, 19-nortestosterone, produced by prepubertal boar testes and its physiological role, normalized complementary DNA (cDNA) from boar testes was generated. DNA sequencing of 2,016 randomly selected clones yielded 794,116 base pairs of high quality nucleotide sequence. Computer-assisted assembly of the nucleotide sequence of each clone resulted in 423 contigs and 403 singletons including several genes for steroidogenic enzymes and molecules related to steroid metabolism. Analysis of gene expression pattern by use of the presently-fabricated cDNA microarray identified a number of genes that were differentially expressed during the postnatal development period in boar testes. Two genes of unknown function were identified to be highly expressed in the testis of 2-weeks-old neonatal boar. In addition, the sequencing of open reading frames of these genes revealed their homology with human alpha hemoglobin and Homo sapiens hypothetical LOC643669, transcript variant 1. Moreover, the transcripts of these genes were also detected in porcine muscle and adipocytes, in addition to Leydig cells of pigs.

• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.534-538
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• 2007

Avermectin and its analogs are major commercial antiparasitic agents in the fields of animal health, agriculture, and human infections. To increase our understanding about the genetic mechanism underlying avermectin overproduction, comparative transcriptomes were analyzed between the low producer S. avermitilis ATCC31267 and the high producer S. avermitilis ATCC31780 via a S. avermitilis whole genome chip. The comparative transcriptome analysis revealed that fifty S. avermitilis genes were expressed at least two-fold higher in S. avermitilis ATCC31780. In particular, all the avermectin biosynthetic genes, including polyketide synthase (PKS) genes and an avermectin pathway-specific regulatory gene, were less expressed in the low producer S. avermitilis ATCC31267. The present results imply that avermectin overproduction in S. avermitilis ATCC31780 could be attributed to the previously unidentified fifty genes reported here and increased transcription levels of avermectin PKS genes.

• Molecular & Cellular Toxicology
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• v.2 no.3
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• pp.185-192
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• 2006

To elucidate the molecular mechanisms associated with early renal injury induced by gentamicin, the most commonly used antibiotics worldwide in the treatment of Gram-negative bacterial infections. We have identified genes differentially expressed at different duration of gentamicin administration. C57BL/6 female mice were treated daily with gentamicin (20 mg/kg, 100 mg/kg, and 200mg/kg) for 7 days and then sacrificed at day 1, 3, and 7 after administration. Standard blood biochemistry and histopathological observation indicative of nephrotoxicity were made. Total RNA was extracted from the kidney for microarray analysis using Affymetrix $GeneChip^{\circledR}$. Five hundred and seventy eight genes were identified as being either up-or down-regulated over 2-fold changes during early renal injury (p<0.05) and were analyzed by hierarchical clustering. The results showed that the genes involved in early immune responses were differentially regulated during early renal injury. Principal component analysis (PCA) confirmed sample separation according to the degree of renal toxicity. In addition, we identified two potential biomarkers that may predict early renal toxicity. This data may contribute to elucidate of the genetic events during early renal injury and to discover the potential biomarkers for nephrotoxicity induced by gentamicin.

• 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.

• Mycobiology
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• v.38 no.2
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• pp.144-148
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• 2010

$\beta$-Glucans have been known to exhibit antitumor activities by potentiating host immunity by an unknown mechanism. The C-type lectin dectin-1, a $\beta$-glucan receptor, is found on the macrophage and can recognize various $\beta$-glucans. Previously, we demonstrated the presence of $\beta$-glucan receptor, dectin-1, on the Raw 264.7 cells as well as on murine mucosal organs, such as the thymus, the lung, and the spleen. In order to investigate immunopotentiation of innate immunity by $\beta$-glucan, we stimulated a murine macrophage Raw 264.7 cell line with $\beta$-glucans from Pleurotus ostreatus, Saccharomyces cerevisiae, and Laminaria digitata. Then, we analyzed cytokines such as tumor necrosis factor (TNF)-$\alpha$ and interleukin (IL)-6 by reverse transcription-polymerase chain reaction (RT-PCR). In addition we analyzed gene expression patterns in $\beta$-glucan-treated Raw 264.7 cells by applying total mRNA to cDNA microarray to investigate the expression of 7,000 known genes. When stimulated with $\beta$-glucans, the macrophage cells increased TNF-$\alpha$ expression. When co-stimulation of the cells with $\beta$-glucan and lipopolysaccharide (LPS), a synergy effect was observed by increased TNF-$\alpha$ expression. In IL-6 expression, any of the $\beta$-glucans tested could not induce IL-6 expression by itself. However, when co-stimulation occurred with $\beta$-glucan and LPS, the cells showed strong synergistic effects by increased IL-6 expression. Chip analysis showed that $\beta$-glucan of P. ostreatus increased gene expressions of immunomodulating gene families such as kinases, lectin associated genes and TNF-related genes in the macrophage cell line. Induction of TNF receptor expression by FACS analysis was synergized only when co-stimulated with $\beta$-glucan and LPS, not with $\beta$-glucan alone. From these data, $\beta$-glucan increased expressions of immunomodulating genes and showed synergistic effect with LPS.

• Journal of Acupuncture Research
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• v.24 no.1
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• pp.151-163
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• 2007

Objectives : Juglandis Semen herbal acupuncture solution(JSS) has a broad array of clinical applications in oriental medicine, including treatment of chronic musculoskeletal diseases such as arthritis. This study was performed to investigate the global gene expression profiles using microarray assay in RAW 264.7 cell line treated with JSS and to advance our understanding of the pharmacologic effect of JSS. Methods : Change of the gene expression profile in RAW cell line following treatment with lipopolysaccharide(LPS) alone, or with LPS plus JSS was investigated with a cut-off level of 2 fold change in the expression. Especially, Change of the gene expression by treatment with LPS alone was compared with that by treatment with LPS plus JSS with a cut-off level of 1/2 fold change in the expression. Results: Of the 8170 genes profiled in this study, 51 were upragulated and 21 downregulated following LPS treatment, and 88 were upregulated and 69 downregulated following costimulation of JSS and LPS. Of the 51 genes upregulated following LPS treatment, 10 were downregulated following costimulation of JSS and LPS. Of the 21 genes downregulated following LPS treatment, 3 were upregulated following costimulation of JSS and LPS. Conclusion : JSS treatment induced upregulation of some genes including IL-10 and downregulation of that including MMP13 with its possible implication in an antiinflammatory action of JSS. However, further research on expression profile changes induced by JSS treatment is expected.

• Molecular & Cellular Toxicology
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• v.2 no.3
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• pp.193-201
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• 2006

Cephalexin, one of most widely prescribed cephalosporin, has been reported to cause acute renal failure as a side effect in human and experimental animals. Although numerous animal studies have been reported for the cephalosporin nephrotoxicity, the molecular and cellular nephrotoxic mechanisms of cephalexin are still unknown. This investigation evaluated the time-dependent gene expression profile of kidney in mouse during cephalexin induced nephrotoxicity. C57BL/6 female mice were administered either saline or 1,000 mg/kg cephalexin intraperitoneally. Mice were sacrificed at 3, 6, and 24 hr after administration. Blood biochemical and histopathological results indicated cephalexin induced nephrotoxicity. Microarray experiment carried out using Affymetrix $GeneChip^{(R)}$. There were 198 informative genes that were significantly expressed >5-fold versus control at 3, 6, and 24 hr (p<0.01), of which 156 and 42 were up-and down-regulated, respectively. Major classes of up-regulated genes at 3, 6 hr included those involved in MAPK/Jak-STAT signaling pathway and immune response such as cytokine-cytokine receptor interaction and complement and coagulation cascades. At 24 hr, up-regulated genes were mainly involved in regeneration/repair and immune response; down-regulated genes were generally associated with transporters and intermediary metabolism. Among the up-regulated genes at 24 hr, several potential biomarkers on nephrotoxicity such as Kim-1, Fga, Timp1, and Slc34a2 were clustered in a same category. In addition, Tnfrsf12a and Lcn2 which were consistently up-regulated (>5 fold) were also included as potential biomarkers. These results may provide clues for elucidating the mechanism of cephalexin induced nephrotoxicity and evaluating potential biomarkers to assess nephrotoxicity.