1.Identification of Matrix Mineralization-Related Genes in Human Periodontal Ligament Cells Using cDNA Microarray.
Jae Hee SHIN ; Jin Woo PARK ; Shin Il YEO ; Woo Chang NOH ; Moon Kyu KIM ; Jung Chul KIM ; Jo Young SUH
The Journal of the Korean Academy of Periodontology 2007;37(Suppl):447-463
No abstract available.
Apoptosis
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DNA, Complementary*
;
Humans*
;
Oligonucleotide Array Sequence Analysis*
;
Periodontal Ligament*
2.An Iterative Normalization Algorithm for cDNA Microarray Medical Data Analysis.
Yoonhee KIM ; Woong Yang PARK ; Ho KIM
Genomics & Informatics 2004;2(2):92-98
No Abstract available.
DNA, Complementary*
;
Oligonucleotide Array Sequence Analysis*
;
Statistics as Topic*
3.Several Genes Expressed During Morphogenesis of Lentinus edodes (ImHyup-1).
Sang Sun LEE ; Sung Woon HONG ; Seung Hae KIM ; Bong Cheol KIM
Mycobiology 2001;29(3):135-141
Differential display of reverse transcription (DDRT)-PCR was conducted to have a profile of the differentially expressed genes during the formation of fruiting body of Lentinus edodes. The lines of L. edodes (ImHyup-1) employed were cultivated in the artificial blocks of sawdust, and the fruiting body was induced from the mycelia or the mass protruded from the brown surface of the sawdust blocks. RNAs were prepared from the four different developmental stages; mycelial, primordial, and stipes and pileus of fruiting body. The fragments of cDNA were synthesized from the combinations of the arbitrary primers and 3' one anchored Oligo-dT primer. Twelve combinations using the primers have been tested, and among them nineteen bands were identified as differentially expressed. Those genes were further analyzed by DNA sequencing and followed by homology search. Characterization of one clone was conducted as a preliminary data and more are under investigation.
Clone Cells
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DNA, Complementary
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Fruit
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Lentinula*
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Morphogenesis*
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Reverse Transcription
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RNA
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Sequence Analysis, DNA
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Shiitake Mushrooms*
4.Development of gene microarray in screening differently expressed genes in keloid and normal-control skin.
Wei CHEN ; Xiao-bing FU ; Shi-li GE ; Xiao-qing SUN ; Gang ZHOU ; Zhi-li ZHAO ; Zhi-yong SHENG
Chinese Medical Journal 2004;117(6):877-881
BACKGROUNDKeloid is an intricate lesion that is probably regulated by many genes. In this study, the authors used the technique of complementary DNA (cDNA) microarray to analyse abnormal gene expression in keloids and normal control skins.
METHODSThe polymerase chain reaction (PCR) products of 8400 genes were spotted in an array on chemical-material-coated-glass plates. The DNAs were fixed on the glass plates. The total RNAs were isolated from freshly excised human keloid and normal control skins, and the mRNAs were then purified. The mRNA from both keloid and normal control skins were reversely transcribed to cDNAs, with the incorporation of fluorescent dUTP, for preparing the hybridisation probes. The mixed probes were then hybridised to the cDNA microarray. After thorough washing, the cDNA microarray was scanned for differing fluorescent signals from two types of tissues. Gene expression of tissue growth factor-beta1 (TGF-beta1) and of c-myc was detected with both RT-PCR and Northern blot hybridisation to confirm the effectiveness of cDNA microarray.
RESULTSAmong the 8400 human genes, 402 were detected with different expression levels between keloid and normal control skins. Two hundred and fifty genes, including TGF-beta1 and c-myc, were up-regulated and 152 genes were down-regulated. Higher expressions of TGF-beta1 and c-myc in keloid were also revealed using RT-PCR and Northern blot methods.
CONCLUSIONcDNA microarray analysis provides a powerful tool for investigating differential gene expression in keloid and normal control skins. Keloid is a complicated lesion with many genes involved.
DNA, Complementary ; analysis ; Humans ; Keloid ; genetics ; Oligonucleotide Array Sequence Analysis ; methods ; Polymerase Chain Reaction ; RNA, Messenger ; analysis ; Skin
5.Early Experience with a cDNA Microarray in Colorectal Cancer.
Chung Su KEUM ; Ryung Ah LEE ; Young Joon HONG ; Seok Il HONG ; Dae Yong HWANG
Journal of the Korean Society of Coloproctology 2003;19(6):341-348
PURPOSE: A cDNA microarray is a systematic method to identify key molecules for prognosis and for treatment response by profiling thousands of genes expressed in a single cancer. The clinical value of cDNA microarray is still being investigated in various fields. This technique could be used in detecting molecules important for cancer to develop, to monitor the effect of new cancer therapeutics, and to give a prognosis for cancer patients. We now report the results of our initial cDNA microarray data to analyze the genome pattern of colorectal cancer tissues and to evaluate the possibility of using cDNA microarrays in a clinical setting for cancer patients. METHODS: We used the general cDNA microarray technique with a 2.4 K cDNA chip provided by Macrogene company. RNA extracted from seven colorectal cancer tissues was amplified by using RT-PCR (reverse transcriptase-polymerase chain reaction), and applied to a cDNA chip to produce an antigen-antibody reaction. The results were analyzed individually and hierarchically. RESULTS: All seven tested cancer tissues were harvested from operative specimens at the Korea Cancer Center Hospital. The male-to-female ratio was 4 to 3. Five patients were TNM stage II, and two patients were stage III. Eighteen genes were upregulated in stage II patients, and 51 in stage III patients. The number of genes discriminating stage was 69, including 8 control genes, 4 ribosomal genes, 5 EST genes, 10 known non-functional genes, 23 genesof unknown function, and 19 possible cancer-related genes. A hierarchial graph showed similar patterns within a stage, which suggests that genetic patterns might affect clinical characteristics. CONCLUSIONS: Seven colorectal cancer tissues were analyzed with the cDNA microarray technique using 2.4 K cDNA chip. Authors could identify 69 genes that showed the significant change of expression. Although our reports presented the preliminary results, we think that the cDNA microarray will be able to offer an informative results to predict cancer development and progression in colorectal cancer.
Antigen-Antibody Reactions
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Colorectal Neoplasms*
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DNA, Complementary*
;
Genome
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Humans
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Korea
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Oligonucleotide Array Sequence Analysis*
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Prognosis
;
RNA
6.Characterization of Differentially Expressed Genes upon Chronic Fluoxetine Treatment in Rat C6 Glioma Cells.
Mi Ran CHOI ; Seung Youn BAIK ; Kyoung Hwa JUNG ; Young Gyu CHAI ; Seok Hyeon KIM ; Sungwon ROH ; Jun Seok LEE ; Dong Yul OH ; Ihn Geun CHOI ; Byung Hwan YANG
Korean Journal of Psychopharmacology 2004;15(4):457-467
OBJECTIVE: The aim of this study was to identify diffrentially regulated genes after the treatment of fluoxetine in rat C6 glioma cells using cDNA microarray chip techniques and real-time RT-PCR. METHODS: Cells were incubated for 24 hours, and for 72 hours with or without 10 uM fluoxetine. Total RNAs extracted from cells were reversely transcribed to cDNA. These cDNA were used to carry out cDNA microarray chip. A part of the up-/down-regulated genes in cDNA microarray result were confirmed by real-time RT-PCR. RESULTS: 1) Genes in fluoxetinetreated cells for 72 hours (chronic treatment) were more regulated than that in fluoxetine-treated cells for 24 hours (acute treatment). 2) The expression level of Gs gene in fluoxetine-treated cells for 24 hours hardly altered, but that of Gs in fluoxetine-treated cells for 72 hours significantly increased. The expression of Gi2 also decreased in 72 hours in relation to 24 hours after the administration of fluoxetine. 3) The expression level of NCAM140 gene in fluoxetine-treated cells was higher than that in control cells. CONCLUSION: We identified genes (Gs, Gi2 and NCAM140) related to neural plasticity and intracellular signal transduction cascade from our result. This implies that fluoxetine may inhibit atrophy or death of impaired neural cells by promoting neurite outgrowth.
Animals
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Atrophy
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DNA, Complementary
;
Fluoxetine*
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Glioma*
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Neurites
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Oligonucleotide Array Sequence Analysis
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Plastics
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Rats*
;
RNA
;
Signal Transduction
7.cDNA Microarray Experiment: Design Issues in Early Stage and the Need of Normalization.
Byung Soo KIM ; Sunho LEE ; Sun Young RHA ; Hyun Cheol CHUNG
Cancer Research and Treatment 2003;35(6):533-540
PURPOSE: The cDNA microarray has become a useful tool for observing the expression of thousands of genes simultaneously. However, obtaining good quality microarray data is not easy due to the inherent noise at various stages of the experiment. Therefore, it is essential to understand the source of the variation in the microarray experiment and its size as an initial step of the data analyses. MATERIALS AND METHODS: The total RNA extracted from HT-1080 fibrosarcoma and normal rat tissues were hybridized to the cDNA microarrays with 0.5 K human and 5 K rat genes, respectively. A homotypic reaction and dye swap experiments were used to identify the sources of the variation. RESULTS: The relative fluorescent intensities of the microarray, if unnormalized, have a large variation, particularly in the lower intensity region. The distribution of the log intensity ratios also exhibit some departure from a band around zero, which is the distribution pattern expected when the majority of genes in the microarray are not regulated. Normalization of the log ratios is usually required as a means of preprocessing the data. We claim that a within-print tip group, an intensity-dependent normalization through a loess fit adjustment will be useful for this purpose, particularly in the initial stages of the microarray experiment. CONCLUSION: For proper data analysis, an understanding the source of the variation and preprocessing of data with a suitable normalization method will be important. It is important to have an interactive cooperation between a researcher and a statistician from the early stages of the study design and to the final stages of data analysis.
Animals
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DNA, Complementary*
;
Fibrosarcoma
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Humans
;
Noise
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Oligonucleotide Array Sequence Analysis*
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Rats
;
RNA
;
Statistics as Topic
8.Global Analysis of Estrogen-Regulated Genes in Mouse Uterus using cDNA Microarray and Laser Capture Microdissection.
Seok Ho HONG ; Hee Young NAH ; Ji Yoon LEE ; Chung Hoon KIM ; Moon Kyoo KIM
Korean Journal of Fertility and Sterility 2003;30(2):151-164
No abstract available.
Animals
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DNA, Complementary*
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Estrogens
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Laser Capture Microdissection*
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Mice*
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Oligonucleotide Array Sequence Analysis*
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Uterus*
9.Global Analysis of Estrogen-Regulated Genes in Mouse Uterus using cDNA Microarray and Laser Capture Microdissection.
Seok Ho HONG ; Hee Young NAH ; Ji Yoon LEE ; Chung Hoon KIM ; Moon Kyoo KIM
Korean Journal of Fertility and Sterility 2003;30(2):151-164
No abstract available.
Animals
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DNA, Complementary*
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Estrogens
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Laser Capture Microdissection*
;
Mice*
;
Oligonucleotide Array Sequence Analysis*
;
Uterus*
10.Using a cDNA microarray to study cellular gene expression altered by Mycobacterium tuberculosis.
Yongzhong XU ; Jianping XIE ; Yao LI ; Jun YUE ; Jianping CHEN ; Lijuan CHUNYU ; Honghai WANG
Chinese Medical Journal 2003;116(7):1070-1073
OBJECTIVETo examine the global effects of Mycobacterium tuberculosis (M. tuberculosis) infection on macrophages.
METHODSThe gene expression profiling of macrophage U937, in response to infection with M. tuberculosis H(37)R(a), was monitored using a high-density cDNA microarray.
RESULTSM. tuberculosis infection caused 463 differentially expressed genes, of which 366 genes are known genes registered in the Gene Bank. These genes function in various cellular processes including intracellular signalling, cytoskeletal rearrangement, apoptosis, transcriptional regulation, cell surface receptors, cell-mediated immunity as well as a variety of cellular metabolic pathways, and may play key roles in M. tuberculosis infection and intracellular survival.
CONCLUSIONSM. tuberculosis infection alters the expression of host-cell genes, and these genes will provide a foundation for understanding the infection process of M. tuberculosis. The cDNA microarray is a powerful tool for studying pathogen-host cell interaction.
Cells, Cultured ; DNA, Complementary ; genetics ; Gene Expression ; Macrophages ; Oligonucleotide Array Sequence Analysis ; Tuberculosis ; genetics