• Title/Summary/Keyword: Gene Expression

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Finding Informative Genes From Microarray Gene Expression Data Using FIGER-test

  • Choi, Kyoung-Oak;Chung, Hwan-Mook
    • Journal of the Korean Institute of Intelligent Systems
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    • v.17 no.5
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    • pp.707-711
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    • 2007
  • Microarray gene expression data is believed to show the functions of living organism through the gene expression values. We have studied a method to get the informative genes from the microarray gene expression data. There are several ways for this. In recent researches to get more sophisticated and detailed results, it has used the intelligence information theory like fuzzy theory. Some methods are to add fudge factors to the significance test for more refined results. In this paper, we suggest a method to get informative genes from microarray gene expression data. We combined the difference of means between two groups and the fuzzy membership degree which reflects the variance of the gene expression data. We have called our significance test the Fuzzy Information method for Gene Expression data(FIGER). The FIGER calculates FIGER variation ratio and FIGER membership degree to show how strongly each object belongs to the each group and then it results in the significance degree of each gene. The FIGER is focused on the variation and distribution of the data set to adjust the significance level. Out simulation shows that the FIGER-test is an effective and useful significance test.

Hierarchical Clustering of Gene Expression Data Based on Self Organizing Map (자기 조직화 지도에 기반한 유전자 발현 데이터의 계층적 군집화)

  • Park, Chang-Beom;Lee, Dong-Hwan;Lee, Seong-Whan
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • pp.170-177
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    • 2003
  • Gene expression data are the quantitative measurements of expression levels and ratios of numberous genes in different situations based on microarray image analysis results. The process to draw meaningful information related to genomic diseases and various biological activities from gene expression data is known as gene expression data analysis. In this paper, we present a hierarchical clustering method of gene expression data based on self organizing map which can analyze the clustering result of gene expression data more efficiently. Using our proposed method, we could eliminate the uncertainty of cluster boundary which is the inherited disadvantage of self organizing map and use the visualization function of hierarchical clustering. And, we could process massive data using fast processing speed of self organizing map and interpret the clustering result of self organizing map more efficiently and user-friendly. To verify the efficiency of our proposed algorithm, we performed tests with following 3 data sets, animal feature data set, yeast gene expression data and leukemia gene expression data set. The result demonstrated the feasibility and utility of the proposed clustering algorithm.

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Gene expression pattern during osteogenic differentiation of human periodontal ligament cells in vitro

  • Choi, Mi-Hye;Noh, Woo-Chang;Park, Jin-Woo;Lee, Jae-Mok;Suh, Jo-Young
    • Journal of Periodontal and Implant Science
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    • v.41 no.4
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    • pp.167-175
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    • 2011
  • Purpose: Periodontal ligament (PDL) cell differentiation into osteoblasts is important in bone formation. Bone formation is a complex biological process and involves several tightly regulated gene expression patterns of bone-related proteins. The expression patterns of bone related proteins are regulated in a temporal manner both in vivo and in vitro. The aim of this study was to observe the gene expression profile in PDL cell proliferation, differentiation, and mineralization in vitro. Methods: PDL cells were grown until confluence, which were then designated as day 0, and nodule formation was induced by the addition of 50 ${\mu}g$/mL ascorbic acid, 10 mM ${\beta}$-glycerophosphate, and 100 nM dexamethasone to the medium. The dishes were stained with Alizarin Red S on days 1, 7, 14, and 21. Real-time polymerase chain reaction was performed for the detection of various genes on days 0, 1, 7, 14, and 21. Results: On day 0 with a confluent monolayer, in the active proliferative stage, c-myc gene expression was observed at its maximal level. On day 7 with a multilayer, alkaline phosphatase, bone morphogenetic protein (BMP)-2, and BMP-4 gene expression had increased and this was followed by maximal expression of osteocalcin on day 14 with the initiation of nodule mineralization. In relationship to apoptosis, c-fos gene expression peaked on day 21 and was characterized by the post-mineralization stage. Here, various genes were regulated in a temporal manner during PDL fibroblast proliferation, extracellular matrix maturation, and mineralization. The gene expression pattern was similar. Conclusions: We can speculate that the gene expression pattern occurs during PDL cell proliferation, differentiation, and mineralization. On the basis of these results, it might be possible to understand the various factors that influence PDL cell proliferation, extracellular matrix maturation, and mineralization with regard to gene expression patterns.

Protective Effect of Polygonum Multiflorum on Cell Damage in UVB-irradiated HaCaT Keratinocytes (적하수오(赤何首烏)의 UVB로 자극한 피부 각질세포 보호 작용)

  • Lee, Seung-Ah;Yoo, Dong-Youl
    • The Journal of Korean Obstetrics and Gynecology
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    • v.24 no.4
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    • pp.31-49
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    • 2011
  • Objectives: This study was performed to assess the protective effect of Polygonum multiflorum(PM) on UVB-irradiated HaCaT Keratinocytes damage. Methods: The protective effects of Polygonum multiflorum(PM) were determined by UVB-irradiated HaCaT assay. We assessed protective effects of Polygonum multiflorum(PM) on LDH release and nitrite production from HaCaT. COX-2, Bcl-2, Bax, $TNF{\alpha}$, c-jun, c-fos, NF-${\kappa}B$, iNOS, Bcl-xL gene expression were determined in HaCaT using real-time PCR method. Results: 1. PM inhibited LDH Release in UVB-irradiated HaCaT Keratinocytes. 2. PM inhibited Nitrite Production in UVB-irradiated HaCaT Keratinocytes. 3. PM suppressed the Gene Expression of COX-2 in UVB-irradiated HaCaT Keratinocytes. 4. PM increased the Gene Expression of Bcl-2 in UVB-irradiated HaCaT Keratinocytes. 5. PM didn't increase the Gene Expression of Bax in UVB-irradiated HaCaT Keratinocytes. 6. PM suppressed the Gene Expression of $TNF{\alpha}$ in UVB-irradiated HaCaT Keratinocytes. 7. PM suppressed the Gene Expression of c-jun in UVB-irradiated HaCaT Keratinocytes. 8. PM suppressed the Gene Expression of c-fos in UVB-irradiated HaCaT Keratinocytes. 9. PM suppressed the Gene Expression of NF-${\kappa}B$ in UVB-irradiated HaCaT Keratinocytes. 10. PM suppressed the Gene Expression of i-NOS in UVB-irradiated HaCaT Keratinocytes. 11. PM didn't increase the Gene Expression of Bcl-xL in UVB-irradiated HaCaT Keratinocytes Conclusions: In conclusion, these results suggest that PM inhibited the cell damage in UVB-irradiated HaCaT.

Cell Free EGFR mRNA Expression and Implications for Survival and Metastasis in Non-Small Cell Lung Cancer Cases

  • Masroor, Mirza;Mir, Rashid;Javid, Jamsheed;Prasant, Y;Imtiyaz, A;Mariyam, Z;Mohan, Anant;Ray, PC;Saxena, Alpana
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.15
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    • pp.6445-6449
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    • 2015
  • Background: NSCLC is a disease involving uncontrolled cell growth, which could result in metastases into nearby tissues beyond the lungs. Materials and Methods: The aim of the present study was to analyze the influence of epidermal growth factor receptor (EGFR) gene expression on metastasis and survival in NSCLC patients. The present case-control study included 100 cases of NSCLC patients and 100 age and sex matched controls. EGFR gene expression was analyzed by quantitative real time PCR using serum RNA. Association with NSCLC patient survival was analyzed by the Kaplan-Meier method. Results: We analyzed EGFR gene expression and observed mean increased gene expression of 13.5 fold in NSCLC patients. Values reflected overall survival of patients with a median of 15.8 months in the cases of <13 fold increased gene expression vs 6.7 months with >13 fold increased EGFR gene expression (p=0.005). Distant metastatic patients with <13 fold increased EGFR gene expression had 7.9 months of median survival time while>13 fold increased EGFR gene expression had only 5 months of median survival time (p=0.03). Non metastatic patients with <13 fold increased EGFR gene expression had 18 months of median survival time as compared to only 7.1 months with >13 fold increased expression. Conclusions: Higher cell free EGFR mRNA expression may play an important role in causing distant metastases and reducing overall survival of NSCLC patients in the Indian population.

Regulation of Gene Expression in Higher Plant (고등식물의 유전자 발현의 조절)

  • 심웅섭
    • Proceedings of the Botanical Society of Korea Conference
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    • pp.241-260
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    • 1987
  • The regulatory mechanisms of gene expression in higher plant were not ascertained in detail because the genome size is very large and complex. However, the above-mentioned study is remarkably progressed in parallel with development of DNA recombinant technology and plant vector system. Some research results connected with the mechanisms could be summarized as follows. 1. Many plant genes including chloroplast genes are cloned. 2. The structures of some regulatory regions of gene expression are determined, and it is confirmed that new regulatory units are made by transposable elements. 3. Plant gene expression is regulated not only at transcriptional level but also at translational level. 4. The factors that regulate plant gene expression could be divided as two categorys. One is endogenous elements including the structural change of chromatin during development stage and tissue differentiation. The other is environmental stimulations such as air, water, heat, salts and light. However, some sufficient research-aid fund is essential in order to study the regulatory mechanisms of gene expression more systematically.

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Gene Expression Pattern Analysis via Latent Variable Models Coupled with Topographic Clustering

  • Chang, Jeong-Ho;Chi, Sung Wook;Zhang, Byoung Tak
    • Genomics & Informatics
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    • v.1 no.1
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    • pp.32-39
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    • 2003
  • We present a latent variable model-based approach to the analysis of gene expression patterns, coupled with topographic clustering. Aspect model, a latent variable model for dyadic data, is applied to extract latent patterns underlying complex variations of gene expression levels. Then a topographic clustering is performed to find coherent groups of genes, based on the extracted latent patterns as well as individual gene expression behaviors. Applied to cell cycle­regulated genes of the yeast Saccharomyces cerevisiae, the proposed method could discover biologically meaningful patterns related with characteristic expression behavior in particular cell cycle phases. In addition, the display of the variation in the composition of these latent patterns on the cluster map provided more facilitated interpretation of the resulting cluster structure. From this, we argue that latent variable models, coupled with topographic clustering, are a promising tool for explorative analysis of gene expression data.

Gene Expression Analysis of Acetaminophen-induced Liver Toxicity in Rat (아세트아미노펜에 의해 간손상이 유발된 랫드의 유전자 발현 분석)

  • Chung, Hee-Kyoung
    • Toxicological Research
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    • v.22 no.4
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    • pp.323-328
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    • 2006
  • Global gene expression profile was analyzed by microarray analysis of rat liver RNA after acute acetaminophen (APAP) administration. A single dose of 1g/kg body weight of APAP was given orally, and the liver samples were obtained after 24, 48 h, and 2 weeks. Histopathologic and biochemical studies enabled the classification of the APAP effect into injury (24 and 48 h) and regeneration (2 weeks) stages. The expression levels of 4900 clones on a custom rat gene microarray were analyzed and 484 clones were differentially expressed with more than a 1.625-fold difference(which equals 0.7 in log2 scale) at one or more time points. Two hundred ninety seven clones were classified as injury-specific clones, while 149 clones as regeneration-specific ones. Characteristic gene expression profiles could be associated with APAP-induced gene expression changes in lipid metabolism, stress response, and protein metabolism. We established a global gene expression profile utilizing microarray analysis in rat liver upon acute APAP administration with a full chronological profile that not only covers injury stage but also later point of regeneration stage.