• Journal of the Korean Data and Information Science Society
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• v.20 no.1
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• pp.171-178
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• 2009

In order to make the high quality Korean cattle, it has been identified the gene which influence to various economic characters. In this paper, we introduce Restricted Partition Method for gene-gene interaction analysis. Further, economic traits, longissimus muscle dorsi area (LMA), carcass cold weight (CWT) and average daily gain (ADG) are applied with Restricted Partition Method (RPM). The SNP (19_1)$^*$SNP (28_2) was selected and was best marker on Single nucleotide polymorphisms (SNPs). It also influenced SNP (19_1)$^*$SNP (28_2) was an very important marker for economic character and to make the thing know it became.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2012.10a
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• pp.991-993
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• 2012

We analyzed RNA polymerase beta subunit gene (rpoB) mutation of rifampin-resistant Mycobacteria through analysis of nucleotide sequence of rpoB DNA (351 bp) containing rifampin resistant region, $rif^r$. For this study, we collected rifampin-resistant Mycobacteria that were identified by conventional culture methods from Masan National Hospital and The Korean Institute of Tuberculosis. We performed sequencing of DNA nucleotides and analyzed rpoB gene of those rifampin-resistant Mycobacteria. From this analysis, we invcestigated diverse mutations of rpoB gene included rifampin-resistant gene, which were not reported, from those rifampin-resistant Mycobacteria.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.18 no.8
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• pp.2017-2022
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• 2014

Novel baculovirus vector systems recombined with coding genes of polyhedron promoter, vesicular stomatitis virus G (VSVG), polyA, cytomegalovirus (CMV) promoter, enhanced green fluorescent protein (EGFP), and protein transduction domain (PTD) were constructed. These recombinant baculovirus vector systems were applied into human foreskin fibroblast cells and compared the effects of gene transfer and gene expression of these recombinant baculovirus vector systems with control vector system. From this study, it showed that these novel recombinant baculovirus vector systems were superior efficacy to control vector system in view of gene transfer and gene expression.

• Communications for Statistical Applications and Methods
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• v.29 no.1
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• pp.65-83
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• 2022

Although various statistical methods have been developed to map time-dependent genetic factors, most identified genetic variants can explain only a small portion of the estimated genetic variation in longitudinal traits. Gene-gene and gene-time/environment interactions are known to be important putative sources of the missing heritability. However, mapping epistatic gene-gene interactions is extremely difficult due to the very large parameter spaces for models containing such interactions. In this paper, we develop a Gaussian process (GP) based nonparametric Bayesian variable selection method for longitudinal data. It maps multiple genetic markers without restricting to pairwise interactions. Rather than modeling each main and interaction term explicitly, the GP model measures the importance of each marker, regardless of whether it is mostly due to a main effect or some interaction effect(s), via an unspecified function. To improve the flexibility of the GP model, we propose a novel grid-based method for the within-subject dependence structure. The proposed method can accurately approximate complex covariance structures. The dimension of the covariance matrix depends only on the number of fixed grid points although each subject may have different numbers of measurements at different time points. The deviance information criterion (DIC) and the Bayesian predictive information criterion (BPIC) are proposed for selecting an optimal number of grid points. To efficiently draw posterior samples, we combine a hybrid Monte Carlo method with a partially collapsed Gibbs (PCG) sampler. We apply the proposed GP model to a mouse dataset on age-related body weight.

• Mycobiology
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• v.41 no.1
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• pp.37-41
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• 2013

Laccases (EC 1.10.3.2) are copper-containing polyphenol oxidases found in white-rot fungi. Here, we report the cloning and analysis of the nucleotide sequence of a new laccase gene, fvlac7, based on the genomic sequence of Flammulina velutipes. A primer set was designed from the putative mRNA that was aligned to the genomic DNA of F. velutipes. A cDNA fragment approximately 1.6-kb long was then amplified by reverse transcriptase-PCR using total RNA, which was subsequently cloned and sequenced. The cDNA sequence of fvlac7 was then compared to that of the genomic DNA, and 16 introns were found in the genomic DNA sequence. The fvlac7 protein, which consists of 538 amino acids, showed only 42~51% identity with 12 different mushroom species containing two laccases of F. velutipes, suggesting the fvlac7 is a novel laccase gene. The first 25 amino acids of Fvlac7 correspond to a predicted signal sequence, four copper-binding sites, and four N-glycosylation sites. Fvlac7 cDNA was heterologously overexpressed in an Escherichia coli system with an approximate expected molecular weight of 60 kDa.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.5
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• pp.3309-3314
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• 2013

Spleen tyrosine kinase (SYK) is a non-receptor type cytoplasmic protein and a known tumor suppressor gene in breast cancer. Polymorphisms in SYK have been reported to be associated with cell invasion/cell morality and an increased risk of cancer development. In this case control study, all exons of the SYK gene and its exon/ intron boundaries were amplified in 200 breast cancer cases and 100 matched controls and then analyzed by single stranded conformational polymorphism. Amplified products showing altered mobility patterns were sequenced and analyzed. Twelve variations were identified in exonic and intronic regions of DNA encoding SH2 domain and kinase domain of the SYK gene. All of these mutations are novel. Among them, 5 missense mutations were observed in exon 15 while one missense mutation was found in exon 8. In addition to these mutations, six mutations were also identified in intronic regions. We found a significant association between SYK mutations and breast cancer and observed that Glu241Arg, a missense mutation is associated with an increase risk of ~7 fold (OR=6.7, 95% CI=1.54-28.8), Thr581Pro (missense mutation) is associated with increased risk of ~16 fold (OR=15.5, 95%CI=2.07-115.45) and 63367 T>G (missense mutation) is associated with increased risk of ~13 fold (OR=12.8, 95%CI=1.71-96.71) for breast cancer. Significant associations were observed for each of these variations with both late menopause (p<0.01) and early menarche (p<0.005) cases when compared to controls. Our findings suggest that the polymorphic gene SYK may contribute to the development of breast cancer in at least the Pakistani population. This study provides an insight view of SYK which may provide a significant finding for the pharmaceutical and biotechnology industry.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.40 no.10
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• pp.2054-2061
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• 2015

Biologically inspired modeling techniques have received considerable attention for their robustness, scalability, and adaptability with simple local interactions and limited information. Among these modeling techniques, Gene Regulatory Networks (GRNs) play a central role in understanding natural evolution and the development of biological organisms from cells. In this paper, we apply GRN principles to the WSN system and propose a new GRN model for decentralized node scheduling design to achieve energy balancing while meeting delay requirements. Through this scheme, each sensor node schedules its state autonomously in response to gene expression and protein concentration, which are controlled by the proposed GRN-inspired node scheduling model. Simulation results indicate that the proposed scheme achieves superior performance with energy balancing as well as desirable delay compared with other well-known schemes.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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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.

• Korean Journal of Veterinary Research
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• v.47 no.2
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• pp.169-174
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• 2007

To provide information for the molecular pathogenesis and antigenic structures of Korean isolates of porcine epidemic diarrhea virus (PEDV), the small membrane (sM) protein gene of Chinju99 strain, which was previously isolated from piglets suffering from severe diarrhea was characterized and further analyzed with other PEDV strains. The sM gene of Chinju99 generated by reverse transcription and polymerase chain reaction had a single open reading frame with 231 bases consisting of 24.2% adenine, 18.6% cytosine, 18.1% guanine and 39.0% thymine nucleotides. Nucleotide sequence of the gene revealed 97.8% homology to those of Belgian strain CV777 and British strain Br1/87, and 97.0% to Chinese strain LZC. The gene encoded a protein with 76 amino acids, and putative amino acid sequence of the gene revealed 98.7% homology to those of CV777 and Br1/87, and 96.1% to LZC. The amino acids of Chinju99 sM gene consisted of mostly hydrophobic residues, and there were one potential N-myristylation site and one potential threonine (T)-linked phosphorylation site recognized. Also, there was a transmembrane region with 46 amino acids, and Chinju99 was more close to CV777 and Br1/87 than to LZC in phylogenetic analysis on the sM amino acid sequences.

• Journal of the Institute of Electronics Engineers of Korea CI
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• v.47 no.5
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• pp.17-24
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• 2010

Recently the study of identifying bio-markers for disease diagnosis and prognosis has been actively performed. In particular, lots of attentions have been paid to the finding of pathway gene-sets differentially expressed in disease patients rather than the finding of individual gene markers. In this paper we propose a novel method to identify disease-related pathway gene-sets based on time-series microarray data. For this purpose, we firstly compute individual gene scores by the using maSigPro (microarray Significant Profiles) and then arrange all the genes in the decreasing order of the corresponding gene scores. The rank of each gene in the entire list is used to evaluate the statistical significance of candidate gene-sets with Wilcoxson rank sum test. For the generation of candidate gene-sets, MSigDB (Molecular Signatures Database) pathway information has been employed. The experiment was conducted with prostate cancer time-series microarray data and the results showed the usefulness of the proposed method by correctly identifying 6 out of 7 biological pathways already known as being actually related to prostate cancer.