• Genomics & Informatics
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• v.5 no.4
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• pp.179-187
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• 2007

An increasing number of primate genomes are being sequenced. A direct comparison of repeat elements in human genes and their corresponding chimpanzee orthologs will not only give information on their evolution, but also shed light on the major evolutionary events that shaped our species. We have developed REPEATOME to enable visualization and subsequent comparisons of human and chimpanzee repeat elements. REPEATOME (http://www.repeatome.org/) provides easy access to a complete repeat element map of the human genome, as well as repeat element-associated information. It provides a convenient and effective way to access the repeat elements within or spanning the functional regions in human and chimpanzee genome sequences. REPEATOME includes information to compare repeat elements and gene structures of human genes and their counterparts in chimpanzee. This database can be accessed using comparative search options such as intersection, union, and difference to find lineage-specific or common repeat elements. REPEATOME allows researchers to perform visualization and comparative analysis of repeat elements in human and chimpanzee.

• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.9-9
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• 2014

Null mutants generated by targeted gene replacement are frequently used to reveal function of the genes in fungi. However, targeted gene deletions may be difficult to obtain or it may not be applicable, such as in the case of redundant or lethal genes. Constitutive expression system could be an alternative to avoid these difficulties and to provide new platform in fungal functional genomics research. Here we developed a novel platform for functional analysis genes in Magnaporthe oryzae by constitutive expression under a strong promoter. Employing a binary vector (pGOF1), carrying $EF1{\beta}$ promoter, we generated a total of 4,432 transformants by Agrobacterium tumefaciens-mediated transformation. We have analyzed a subset of 54 transformants that have the vector inserted in the promoter region of individual genes, at distances ranging from 44 to 1,479 bp. These transformants showed increased transcript levels of the genes that are found immediately adjacent to the vector, compared to those of wild type. Ten transformants showed higher levels of expression relative to the wild type not only in mycelial stage but also during infection-related development. Two transformants that T-DNA was inserted in the promotor regions of putative lethal genes, MoRPT4 and MoDBP5, showed decreased conidiation and pathogenicity, respectively. We also characterized two transformants that T-DNA was inserted in functionally redundant genes encoding alpha-glucosidase and alpha-mannosidase. These transformants also showed decreased mycelial growth and pathogenicity, implying successful application of this platform in functional analysis of the genes. Our data also demonstrated that comparative phenotypic analysis under over-expression and suppression of gene expression could prove a highly efficient system for functional analysis of the genes. Our over-expressed transformants library would be a valuable resource for functional characterization of the redundant or lethal genes in M. oryzae and this system may be applicable in other fungi.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2006.10a
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• pp.451-452
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• 2006

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.9 no.1
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• pp.36-41
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• 2009

Self organizing map(SOM) is one of the unsupervised methods based on the competitive learning. Many clustering works have been performed using SOM. It has offered the data visualization according to its result. The visualized result has been used for decision process of descriptive data mining as exploratory data analysis. In this paper we propose improvement of SOM using stratified sampling of statistics. The stratification leads to improve the performance of SOM. To verify improvement of our study, we make comparative experiments using the data sets form UCI machine learning repository and simulation data.

• Genomics & Informatics
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• v.5 no.3
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• pp.129-132
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• 2007

arraylmpute is a software for exploratory analysis of missing data and imputation of missing values in microarray data. It also provides a comparative analysis of the imputed values obtained from various imputation methods. Thus, it allows the users to choose an appropriate imputation method for microarray data. It is built on R and provides a user-friendly graphical interface. Therefore, the users can easily use arraylmpute to explore, estimate missing data, and compare imputation methods for further analysis.

• Proceedings of the Malacological Society of Korea Conference
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• 2005.07a
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• pp.21-21
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• 2005

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.12
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• pp.1649-1659
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• 2012

Crosses between Korean and Landrace pigs have revealed a large quantitative trait loci (QTL) region for fat deposition in a region (89 cM) of porcine chromosome 4 (SSC4). To more finely map this QTL region and identify candidate genes for this trait, comparative mapping of pig and human chromosomes was performed in the present study. A region in the human genome that corresponds to the porcine QTL region was identified in HSA1q21. Furthermore, the LMNA gene, which is tightly associated with fat augmentation in humans, was localized to this region. Radiation hybrid (RH) mapping using a Sus scrofa RH panel localized LMNA to a region of 90.3 cM in the porcine genome, distinct from microsatellite marker S0214 (87.3 cM). Two-point analysis showed that LMNA was linked to S0214, SW1996, and S0073 on SSC4 with logarithm (base 10) of odds scores of 20.98, 17.78, and 16.73, respectively. To clone the porcine LMNA gene and to delineate the genomic structure and sequences, including the 3'untranslated region (UTR), rapid amplification of cDNA ends was performed. The coding sequence of porcine LMNA consisted of 1,719 bp, flanked by a 5'UTR and a 3'UTR. Two synonymous single nucleotide polymorphisms (SNPs) were identified in exons 3 and 7. Association tests showed that the SNP located in exon 3 (A193A) was significantly associated with weight at 30 wks (p<0.01) and crude fat content (p<0.05). This association suggests that SNPs located in LMNA could be used for marker-assisted selection in pigs.

• Journal of Integrative Natural Science
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• v.9 no.2
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• pp.121-127
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• 2016

CXC chemokine receptor 2 (CXCR2) is a prominent chemokine receptor on neutrophils. The neutrophilic inflammation in the lung diseases is found to be largely regulated through CXCR2 receptor. Antagonist of CXCR2 may reduce the neutrophil chemotaxis and alter the inflammatory response. Hence, in the present study, ligand based Comparative molecular field analysis (CoMFA) was performed on a series of CXCR2 antagonist named pyrimidine-5-carbonitrile-6-alkyl derivatives. The optimum CoMFA model was obtained with statistically significant cross-validated coefficients ($q^2$) of 0.568 and conventional coefficients ($r^2$) of 0.975. The contour maps suggest the important structural modifications and this study can be used to guide the development of potent CXCR2 antagonist.

• Journal of Microbiology and Biotechnology
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• v.27 no.8
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• pp.1419-1427
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• 2017

As probiotics play an important role in maintaining a healthy gut flora environment through antitoxin activity and inhibition of pathogen colonization, they have been of interest to the medical research community for quite some time now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in fermented food, are of particular interest given their easy accessibility. We performed whole-genome sequencing and genomic analysis on a GB-LP1 strain of L. plantarum isolated from Korean traditional fermented food; this strain is well known for its functions in immune response, suppression of pathogen growth, and antitoxin effects. The complete genome sequence of GB-LP1 is a single chromosome of 3,040,388 bp with 2,899 predicted open reading frames. Genomic analysis of GB-LP1 revealed two CRISPR regions and genes showing accelerated evolution, which may have antibiotic and antitoxin functions. The aim of the present study was to predict strain specific-genomic characteristics and assess the potential of this new strain as lactic acid bacteria at the genomic level using in silico analysis. These results provide insight into the L. plantarum species as well as confirm the possibility of its utility as a candidate probiotic.

• Journal of Integrative Natural Science
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• v.9 no.2
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• pp.128-135
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• 2016

5-hydroxytryptamine (serotonin) receptor ($5-HT_7R$) 7 is one of G-Protein coupled receptors, which is activated by the neurotransmitter Serotonin. After activation by serotonin, $5-HT_7$ activates the production of the intracellular signaling molecule cyclic AMP. $5-HT_7$ receptor has been found to be involved in the pathophysiology of various disorders. It is reported that $5-HT_7$ receptor antagonists can be used as antidepressant agents. In this study, we report the important structural and chemical parameters for 2-methoxyphenylpiperazinylakanamides as $5-HT_7R$ inhibitors. A 3D QSAR study based on comparative molecular field analysis (CoMFA) was performed. The best predictions were obtained for the best CoMFA model with $q^2$ of 0.594 with 6 components, $r^2$ of 0.986, Fisher value as 60.607, and an estimated standard error of 0.043. The predictive ability of the test set was 0.602. Results obtained the CoMFA models suggest that the data are well fitted and have high predictive ability. The contour maps are generated and studied. The contour analyses may serve as tool in the future for designing of novel and more potent $5-HT_7R$ derivatives.