• Title/Summary/Keyword: 유전자 예측

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Development of an Intelligent Trading System Using Support Vector Machines and Genetic Algorithms (Support Vector Machines와 유전자 알고리즘을 이용한 지능형 트레이딩 시스템 개발)

  • Kim, Sun-Woong;Ahn, Hyun-Chul
    • Journal of Intelligence and Information Systems
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    • v.16 no.1
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    • pp.71-92
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    • 2010
  • As the use of trading systems increases recently, many researchers are interested in developing intelligent trading systems using artificial intelligence techniques. However, most prior studies on trading systems have common limitations. First, they just adopted several technical indicators based on stock indices as independent variables although there are a variety of variables that can be used as independent variables for predicting the market. In addition, most of them focus on developing a model that predicts the direction of the stock market indices rather than one that can generate trading signals for maximizing returns. Thus, in this study, we propose a novel intelligent trading system that mitigates these limitations. It is designed to use both the technical indicators and the other non-price variables on the market. Also, it adopts 'two-threshold mechanism' so that it can transform the outcome of the stock market prediction model based on support vector machines to the trading decision signals like buy, sell or hold. To validate the usefulness of the proposed system, we applied it to the real world data-the KOSPI200 index from May 2004 to December 2009. As a result, we found that the proposed system outperformed other comparative models from the perspective of 'rate of return'.

A Study of the Predictive Effectiveness of Stem and Root Extracts of Cannabis sativa L. Through Network Pharmacological Analysis (네트워크 분석기반을 통한 대마 줄기 및 뿌리 추출물의 약리효능 예측연구)

  • Myung-Ja Shin;Min-Ho Cha
    • Journal of Life Science
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    • v.34 no.3
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    • pp.179-190
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    • 2024
  • Cannabis sativa is a plant widely cultivated worldwide and has been used as a material for food, medicine, building materials and cosmetics. In this study, we assessed the functional effects of C. sativa stem and root extracts using network pharmacology and confirmed their novel functions. The components in stem and root ethanol extracts were identified by gas chromatography-mass spectrometry analysis, and networks between the components and proteins were constructed using the STICHI database. Functional annotation of the proteins was performed using the KEGG pathway. The effects of the extracts were confirmed in lysophosphatidylcholine-induced THP-1 cells using real-time PCR. A total of 21 and 32 components were identified in stem and root extracts, respectively, and 147 and 184 proteins were linked to stem and root components, respectively. KEGG pathway analysis showed that 69 pathways, including the MAPK signaling pathway, were commonly affected by the extracts. Further investigation using pathway networks revealed that terpenoid backbone biosynthesis was likely affected by the extracts, and the expression of the MVK and MVD genes, key proteins in terpenoid backbone biosynthesis, was decreased in LPC-induced THP-1 cells. Therefore, this study determined the diverse function of C. sativa extracts, providing information for predicting and researching the effects of C. sativa.

Correlation of p53 Protein Overexpression, Gene Mutation with Prognosis in Resected Non-Small Cell Lung Cancer(NSCLC) Patients (비소세포폐암에서 p53유전자의 구조적 이상 및 단백질 발현이 예후에 미치는 영향)

  • Lee, Y.H.;Shin, D.H.;Kim, J.H.;Lim, H.Y.;Chung, K.Y.;Yang, W.I.;Kim, S.K.;Chang, J.;Roh, J.K.;Kim, S.K.;Lee, W.Y.;Kim, B.S.;Kim, B.S.
    • Tuberculosis and Respiratory Diseases
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    • v.41 no.4
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    • pp.339-353
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    • 1994
  • Background : The p53 gene codes for a DNA-binding nuclear phosphoprotein that appears to inhibit the progression of cells from the G1 to the S phase of the cell cycle. Mutations of the p53 gene are common in a wide variety of human cancers, including lung cancer. In lung cancers, point mutations of the p53 gene have been found in all histological types including approximately 45% of resected NSCLC and even more frequently in SCLC specimens. Mutant forms of the p53 protein have transforming activity and interfere with the cell-cycle regulatory function of the wild-type protein. The majority of p53 gene mutations produce proteins with altered conformation and prolonged half life; these mutant proteins accumulate in the cell nucleus and can be detected by immunohistochemical staining. But protein overexpression has been reported in the absence of mutation. p53 protein overexpression or gene mutation is reported poor prognostic factor in breast cancer, but in lung cancer, its prognostic significance is controversial. Method : We investigated the p53 abnormalities by nucleotide sequencing, polymerase chain reaction-single strand conformation polymorphism(PCR-SSCP), and immunohistochemical staining. We correlated these results with each other and survival in 75 patients with NSCLC resected with curative intent. Overexpression of the p53 protein was studied immunohistochemically in archival paraffin- embedded tumor samples using the D07(Novocastra, U.K.) antibody. Overexpression of p53 protein was defined by the nuclear staining of greater than 25% immunopositive cells in tumors. Detection of p53 gene mutation was done by PCR-SSCP and nucleotide sequencing from the exon 5-9 of p53 gene. Result: 1) Of the 75 patients, 36%(27/75) showed p53 overexpression by immunohistochemical stain. There was no survival difference between positive and negative p53 immunostaining(overall median survival of 26 months, disease free median survival of 13 months in both groups). 2) By PCR-SSCP, 27.6%(16/58) of the patients showed mobility shift. There was no significant difference in survival according to mobility shift(overall median survival of 27 in patients without mobility shift vs 20 months in patients with mobility shift, disease free median survival of 8 months vs 10 months respectively). 3) Nucleotide sequence was analysed from 29 patients, and 34.5%(10/29) had mutant p53 sequence. Patients with the presence of gene mutations showed tendency to shortened survival compared with the patients with no mutation(overall median survival of 22 vs 27 months, disease free median survival of 10 vs 20 months), but there was no statistical significance. 4) The sensitivity and specificity of immunostain based on PCR-SSCP was 67.0%, 74.0%, and that of the PCR-SSCP based on the nucleotide sequencing was 91.8%, 96.2% respectively. The concordance rate between the immunostain and PCR-SSCP was 62.5%, and the rate between the PCR-SSCP and nucleotide sequencing was 95.3%. Conclusion : In terms of detection of p53 gene mutation, PCR-SSCP was superior to immunostaining. p53 gene abnormalities either overexpression or mutation were not a significant prognostic factor in NSCLC patients resected with curative intent. However, patients with the mutated p53 gene showed the trends of early relapse.

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Diagnostic Utility of MAGE Expression in Exudative Pleural Effusion (삼출성 흉수에서 악성 감별을 위한 MAGE 유전자 검출의 의의)

  • Kim, Kyung Chan;Seo, Chang Gyun;Park, Sun Hyo;Choi, Won-Il;Han, Seung Beom;Jeon, Young June;Park, Jong-Wook;Jeon, Chang-Ho
    • Tuberculosis and Respiratory Diseases
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    • v.56 no.2
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    • pp.159-168
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    • 2004
  • Background : In recent years, numerous human tumor specific antigens such as melanoma antigen gene(MAGE) that is recognized by autologous cytotoxic T lymphocytes have been identified. MAGE is expressed in many human malignancies in various organs, such as lung, breast, stomach, esophagus and leukemia. Therefore MAGE has been studied widely for tumor diagnosis and immunotherapy. But, so far there were no clinical studies evaluating the role of MAGE in pleural effusion. We investigated the expression of MAGE in the patients with exudative pleural effusion for it's diagnostic utility and the results were compared with those of cytologic examinations. Methods : Diagnostic thoracentesis was performed in 44 consecutive patients with exudative pleural effusion during 6 months. We examined the expression of MAGE and cytology with the obtained pleural effusion. Expression of MAGE was interpreted by means of a commercial kit using RT-PCR method. Enrolled patients were divided into two groups such as malignant and benign and we analyzed its' sensitivity and specificity. Results : There were no significant differences between two groups in age, sex, white blood cell counts in pleural fluid, pleural fluid/serum protein ratio and pleural fluid/serum LDH ratio. The sensitivity and specificity of MAGE were 72.2% and 96.2% respectively and the positive predictive value and negative predictive value of MAGE were also 92.9% and 83.3% respectively. The sensitivity and negative predictive value of cytologic examinations were 66.7% and 81.3% respectively. There were no significant differences between sensitivities of MAGE and cytologic examinations but false positive result of MAGE was found in 1 case of tuberculous pleurisy. Conclusion : MAGE is a sensitive and specific marker for the differential diagnosis between benign and malignant effusion in patients with exudative pleural effusion. And MAGE would provide the equal sensitivity compared with that of cytologic examination in patients with malignant pleural effusion if 5mL of the pleural fluid is examined.

Significance of p53 as a Prognostic Factor in Non-Small Cell Lung Carcinoma (비소세포 폐암종에 있어서 p53의 예후 인자로서의 의의)

  • 이상호;한정호;김관민;김진국;심영목;장인석
    • Journal of Chest Surgery
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    • v.37 no.8
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    • pp.672-683
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    • 2004
  • Background: The treatment results of the advanced lung carcinoma is not satisfactory with the present therapeutic modalities: surgical resection, anti-cancer chemotherapy, and radiotherapy or combination therapy. To predict the prognosis of the non-small-cell lung carcinoma, TNM classification has been was as the basic categorization; however, it has been not satisfactory. It is necessary to consider the causes and the prognosis of the lung carcinoma from another points of view rather the conventional methods. We intended to find out the relationship between the major apoptotic factor, p53 gene and the prognosis of the patient with lung carcinoma. Material and Method: Three hundreds and fifty-nine patients with lung carcinoma who underwent surgery were analysed. We observed p53 protein accumulated in the cellular nuclei. The p53 protein was detected by immuno-histo-chemical method. We collected information of the patient retrospectively. Result: p53 protein densities were observed in 40% in average as a whole. The protein density was 44 percent in man, 25 percent in woman, 49 percent in the squamous cell carcinoma, and 38 percent in the adenocarcinoma. There were significant correlations between the p53 protein density and the mortality in the squamous cell carcinoma (p=0.025), follow-up duration in TNM stage I group (p=0.010), and follow-up duration in the lobectomy patient group (p=0.043), and tumor cell differentiation (p=0.009). p53 protein densities were significantly different between the lobectomy and the pneumonectomy group (p=0.044). Conclusion: The authors found that p53 protein had some correlations with the prognosis of the lung cancer partially in some factors. We suggest the p53 protein density could be used as a marker of prognosis in the non-small-cell lung carcinoma.

Pharmacogenetic Impact on Korean Patients Receiving Antiepileptic Drugs (항전간제를 투여받은 한국인 환자에서의 약리유전학적 영향)

  • Kim, Jeong-Oh;Lee, Han-Hee;Shin, Jung-Young;Zhang, Xiang Hua;Oh, Ji-Eun;Kim, Yeong-In;Lee, Jeong-Hyun;Kang, Jin-Hyoung
    • Journal of Life Science
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    • v.22 no.8
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    • pp.1057-1063
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    • 2012
  • Epilepsy is the most prevalent chronic neurological disorder and can be controlled by antiepileptic drugs (AEDs) in up to 70% of patients. We performed an association study between adverse drug reactions and the genetic polymorphisms of CYP2C9, CYP2C19, ABCB1, and SCN1A. The clinical data of 83 epilepsy patients who had received AEDs containing carbamazepine (CBZ) were collected. We extracted genomic DNA from peripheral blood and then genotyped CYP2C9 ($CYP2C9^*2$, $CYP2C9^*3$), CYP2C19 ($CYP2C9^*2$, $CYP2C9^*3$), ABCB1 (C3435T), and SCN1A (IVS5N+5 G>A) using direct sequencing. The allele frequencies of $CYP2C9^*3$, $CYP2C9^*2$, $CYP2C9^*3$, ABCB1 (3435C>T), and SCN1A (IVS5N+5 G>A) were 0.93, 0.72, 0.91, 0.61, and 0.55, respectively. Statistically significant differences were indicated from the data obtained. Patients with SCN1A genotype CC or CT were compared with patients with SCN1A genotype TT while using more than 500mg of carbamazepine. We have associated functional polymorphisms with the dose used in regular clinical practice for Korean epilepsy patients who had received antiepileptic drugs (AEDs) containing carbamazepine. For AEDs, we found that one of the SCN1A genotypes is associated with a 500 mg dose. There was no association found with CNS ADR caused by AEDs.

H2AX Directly Interacts with BRCA1 and BARD1 via its NLS and BRCT Domain Respectively in vitro (H2AX의 BRCA1 NLS domain과 BARD1 BRCT domain 각각과의 in vitro 상호 결합)

  • Bae, Seung-Hee;Lee, Sun-Mi;Kim, Su-Mi;Choe, Tae-Boo;Kim, Cha-Soon;Seong, Ki-Moon;Jin, Young-Woo;An, Sung-Kwan
    • KSBB Journal
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    • v.24 no.4
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    • pp.403-409
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    • 2009
  • H2AX, a crucial component of chromatin, is implicated in DNA repair, cell cycle check point and tumor suppression. The aim of this study was to identify direct binding partners of H2AX to regulate cellular responses to above mechanisms. Literature reviews and bioinformatical tools were attempted intensively to find binding partners of H2AX, which resulted in identifying two potential proteins, breast cancer-1 (BRCA1) and BRCA1-associated RING domain 1 (BARD1). Although it has been reported in vivo that BRCA1 co-localizes with H2AX at the site of DNA damage, their biochemical mechanism for H2AX were however only known that the complex monoubiquitinates histone monomers, including unphosphorylated H2AX in vitro. Therefore, it is important to know whether the complex directly interacts with H2AX, and also which regions of these are specifically mediated for the interaction. Using in vitro GST pull-down assay, we present here that BRCA1 and BARD1 directly bind to H2AX. Moreover, through combinational approaches of domain analysis, fragment clonings and in vitro binding assay, we revealed molecular details of the BRCA1-H2AX and BARD1-H2AX complex. These data provide the potential evidence that each of the BRCA1 nuclear localization signal (NLS) and BARD1 BRCA1 C-terminal (BRCT) repeat domain is the novel mediator of H2AX recognition.

Association between the Human Surfactant Protein-A(SP-A) Gene Locus and Chronic Obstructive Pulmonary Disease in Korean Population (한국인에서 만성폐쇄성폐질환과 인체 폐 표면 활성제 단백-A 유전자 대립형질의 상관관계)

  • Na, Joo Ock;Oh, Myung Ho;Choi, Jae Sung;Seo, Ki Hyun;Kim, Yong Hoon
    • Tuberculosis and Respiratory Diseases
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    • v.60 no.6
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    • pp.638-644
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    • 2006
  • Backgrounds: This study investigated whether or not a polymorphism in the gene encoding the surfactant protein A(SP-A) has any bearing on the individual susceptibility to the development of chronic obstructive pulmonary disease(COPD) in a genetically homogenous Korean population. Methods: The genotypes of 19 COPD patients and 20 healthy neonates as controls were tested using a polymerase chain reaction followed by restriction fragment length polymorphism analysis for the SP-A gene. Results: The specific frequencies of the 6A2 and 6A18 alleles of SP-A1 and the 1A2 allele of SP-A2 were much higher in the COPD group than control group (p<0.05). However, the frequencies of the 6A3 and 6A4 alleles of SP-A1 and the 1A0 allele of SP-A2 in the COPD group were significantly lower than the control group. In the COPD group, the frequencies of the +50 locus genotypes GG of SP-A1 and the +9 locus genotypes CC of SP-A2 were 85.0% and 60.6%, respectively, and 19.7% and 24.8% in the control group, respectively. The frequencies of the polymorphic genotypes or alleles showed a statistically significant difference between the COPD group and the control group (P<0.05). Conclusion: A genetic polymorphism in SP-A is associated with the development of COPD in the Korean population.

Development and application of prediction model of hyperlipidemia using SVM and meta-learning algorithm (SVM과 meta-learning algorithm을 이용한 고지혈증 유병 예측모형 개발과 활용)

  • Lee, Seulki;Shin, Taeksoo
    • Journal of Intelligence and Information Systems
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    • v.24 no.2
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    • pp.111-124
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    • 2018
  • This study aims to develop a classification model for predicting the occurrence of hyperlipidemia, one of the chronic diseases. Prior studies applying data mining techniques for predicting disease can be classified into a model design study for predicting cardiovascular disease and a study comparing disease prediction research results. In the case of foreign literatures, studies predicting cardiovascular disease were predominant in predicting disease using data mining techniques. Although domestic studies were not much different from those of foreign countries, studies focusing on hypertension and diabetes were mainly conducted. Since hypertension and diabetes as well as chronic diseases, hyperlipidemia, are also of high importance, this study selected hyperlipidemia as the disease to be analyzed. We also developed a model for predicting hyperlipidemia using SVM and meta learning algorithms, which are already known to have excellent predictive power. In order to achieve the purpose of this study, we used data set from Korea Health Panel 2012. The Korean Health Panel produces basic data on the level of health expenditure, health level and health behavior, and has conducted an annual survey since 2008. In this study, 1,088 patients with hyperlipidemia were randomly selected from the hospitalized, outpatient, emergency, and chronic disease data of the Korean Health Panel in 2012, and 1,088 nonpatients were also randomly extracted. A total of 2,176 people were selected for the study. Three methods were used to select input variables for predicting hyperlipidemia. First, stepwise method was performed using logistic regression. Among the 17 variables, the categorical variables(except for length of smoking) are expressed as dummy variables, which are assumed to be separate variables on the basis of the reference group, and these variables were analyzed. Six variables (age, BMI, education level, marital status, smoking status, gender) excluding income level and smoking period were selected based on significance level 0.1. Second, C4.5 as a decision tree algorithm is used. The significant input variables were age, smoking status, and education level. Finally, C4.5 as a decision tree algorithm is used. In SVM, the input variables selected by genetic algorithms consisted of 6 variables such as age, marital status, education level, economic activity, smoking period, and physical activity status, and the input variables selected by genetic algorithms in artificial neural network consist of 3 variables such as age, marital status, and education level. Based on the selected parameters, we compared SVM, meta learning algorithm and other prediction models for hyperlipidemia patients, and compared the classification performances using TP rate and precision. The main results of the analysis are as follows. First, the accuracy of the SVM was 88.4% and the accuracy of the artificial neural network was 86.7%. Second, the accuracy of classification models using the selected input variables through stepwise method was slightly higher than that of classification models using the whole variables. Third, the precision of artificial neural network was higher than that of SVM when only three variables as input variables were selected by decision trees. As a result of classification models based on the input variables selected through the genetic algorithm, classification accuracy of SVM was 88.5% and that of artificial neural network was 87.9%. Finally, this study indicated that stacking as the meta learning algorithm proposed in this study, has the best performance when it uses the predicted outputs of SVM and MLP as input variables of SVM, which is a meta classifier. The purpose of this study was to predict hyperlipidemia, one of the representative chronic diseases. To do this, we used SVM and meta-learning algorithms, which is known to have high accuracy. As a result, the accuracy of classification of hyperlipidemia in the stacking as a meta learner was higher than other meta-learning algorithms. However, the predictive performance of the meta-learning algorithm proposed in this study is the same as that of SVM with the best performance (88.6%) among the single models. The limitations of this study are as follows. First, various variable selection methods were tried, but most variables used in the study were categorical dummy variables. In the case with a large number of categorical variables, the results may be different if continuous variables are used because the model can be better suited to categorical variables such as decision trees than general models such as neural networks. Despite these limitations, this study has significance in predicting hyperlipidemia with hybrid models such as met learning algorithms which have not been studied previously. It can be said that the result of improving the model accuracy by applying various variable selection techniques is meaningful. In addition, it is expected that our proposed model will be effective for the prevention and management of hyperlipidemia.

Genome Sequence Analysis of Chrysanthemum White Rust pathogen Puccinia horiana and Sterol 14-demethylase as Drug Target (국화흰녹병균 Puccinia horiana 유전체 분석과 약물 표적으로서의 sterol 14-demethylase)

  • Kim, Jeong-Gu;Park, Sang Kun;Park, Ha-Seung;Kwon, Soo-Jin;Kim, Seung Hwan;Lee, Dong-Jun;Sohn, Seong-Han;Lee, Byoung Moo;Bae, Shin-Chul;Ahn, Il-Pyung;Kim, Changhoon;Baek, Jeong Hun
    • The Korean Journal of Pesticide Science
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    • v.17 no.4
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    • pp.468-472
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    • 2013
  • Chrysanthemum is an economically important horticultural plant in many countries. The white rust is one of the most devastating diseases caused by an obligate fungal pathogen Puccinia horiana. This is being controlled mostly by application of chemicals. In Korea, 26 items are registered and 10 items contain 6 triazole compounds. To identify and to obtain the information of the drug target for triazoles, possible sterol 14-demethylase orthologues were extracted. From the draft genome information, the nucleotide sequence of the sterol 14-demethylase gene was identified. The amino acid sequence was deduced and the tertiary structure of the enzyme was predicted. This protein showed no less than 84% amino acid sequence identities to those of genus Puccinia and no more than 68% to those of other genus.