• Proceedings of the KSRS Conference
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• v.2
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• pp.623-626
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• 2006

Group of genes controls the functioning of a cell by complex interactions. These interacting gene groups are called Gene Regulatory Networks (GRNs). Two previous data mining approaches, clustering and classification have been used to analyze gene expression data. While these mining tools are useful for determining membership of genes by homology, they don't identify the regulatory relationships among genes found in the same class of molecular actions. Furthermore, we need to understand the mechanism of how genes relate and how they regulate one another. In order to detect regulatory relationships among genes from time-series Microarray data, we propose a novel approach using frequent pattern mining and chain rule. In this approach, we propose a method for transforming gene expression data to make suitable for frequent pattern mining, and detect gene expression patterns applying FP-growth algorithm. And then, we construct gene regulatory network from frequent gene patterns using chain rule. Finally, we validated our proposed method by showing that our experimental results are consistent with published results.

• Proceedings of the Korea Information Processing Society Conference
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• 2014.11a
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• pp.849-852
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• 2014

Reverse engineering of gene regulatory network is a challenging task in computational biology. To detect a regulatory relationship among genes from time series data is called reverse engineering. Reverse engineering helps to discover the architecture of the underlying gene regulatory network. Besides, it insights into the disease process, biological process and drug discovery. There are many statistical approaches available for reverse engineering of gene regulatory network. In our paper, we propose pairwise mutual information for the reverse engineering of a gene regulatory network from time series data. Firstly, we create random boolean networks by the well-known $Erd{\ddot{o}}s-R{\acute{e}}nyi$ model. Secondly, we generate artificial time series data from that network. Then, we calculate pairwise mutual information for predicting the network. We implement of our system on java platform. To visualize the random boolean network graphically we use cytoscape plugins 2.8.0.

• The KIPS Transactions:PartD
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• v.14D no.1 s.111
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• pp.9-20
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• 2007

Groups of genes control the functioning of a cell by complex interactions. Such interactions of gene groups are tailed Gene Regulatory Networks(GRNs). Two previous data mining approaches, clustering and classification, have been used to analyze gene expression data. Though these mining tools are useful for determining membership of genes by homology, they don't identify the regulatory relationships among genes found in the same class of molecular actions. Furthermore, we need to understand the mechanism of how genes relate and how they regulate one another. In order to detect regulatory relationships among genes from time-series Microarray data, we propose a novel approach using frequent pattern mining and chain rules. In this approach, we propose a method for transforming gene expression data to make suitable for frequent pattern mining, and gene expression patterns we detected by applying the FP-growth algorithm. Next, we construct a gene regulatory network from frequent gene patterns using chain rules. Finally, we validate our proposed method through our experimental results, which are consistent with published results.

• Animal cells and systems
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• v.1 no.2
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• pp.345-350
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• 1997

The ${\beta}$-Lactoglobulin (BLG) gene expression is differentially regulated during development of the mammary tissues. Such differential regulation of the BLG gene expression can be reiterated in the cultured mammary HC11 cells. In the growing non-confluent HC11 cells, the BLG promoter activity was shown to be partially repressed by the upstream regulatory sequence. The repression was gradually diminished and switched to activation as the cells grew confluent. The differential regulation of the BLG promoter was controlled by the 5'-regulatory sequence located at the upstream of 205 bp. Electromobility shift assay showed that nuclear extract from HC11 cells differentially bound on the regulatory sequence, depending on the cell confluency, which was in accordance with the differential transcriptional activity. DNase I foot-print assay, however, revealed that all nuclear extracts presented the same foot-prints, regardless of confluency of HC11 cells. These results suggest that differential regulation BLG gene expression by the 5'-regulatory sequence may be accomplished by competitive and/or cooperative binding of differential regulatory factors on the same regulatory element.

• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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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.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.11
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• pp.1628-1633
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• 2001

A goat ${\beta}$-casein gene was cloned and sequenced. Our previous study had determined the nucleotide sequences of the 5' flanking region and the structural gene including all 9 exons. In the present study, investigations were done on the regulatory sequences in the 5' flanking region of the goat ${\beta}$-casein gene by aligning and comparing it with the same gene from other mammals. The results showed that -200/-1 bp of the 5' flanking sequences contained six conserved clusters, in which the sites of gene expression regulated by the transcription factor and hormone might exist. It showed that fourteen glucocorticoid receptor elements, two cAMP responsive elements, two SV40 virus enhancer core sequences, two OCT-1 binding elements and one CTF/NF-1 binding element were dispersed in the 5' flanking region of goat ${\beta}$-casein gene. Our findings are perhaps valuable for the elucidation of the molecular mechanisms that control the expression of the goat ${\beta}$-casein gene.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.24-27
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• 2007

Human cell regulatory mechanism is one of suspicious problems among biologists. Here we tried to uncover the human breast cancer cell regulatory mechanism from gene expression data (Marc J. Van de vijver, et. al., 2002) using a module network algorithm which is suggested by Segal, et. al.(2003) Finally, we derived a module network which consists of 50 modules and 10 tree depths. Moreover, to validate this candidate network, we applied a GO enrichment test and known transcription factor-target relationships from Transfac(R) (V. Matys, et. al, 2006) and HPRD database (Peri, S. et al., 2003).

• Journal of Microbiology and Biotechnology
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• v.24 no.9
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• pp.1226-1231
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• 2014

The rare actinomycete Pseudonocardia autotrophica was previously shown to produce a solubility-improved toxicity-reduced novel polyene compound named $\underline{N}ystatin$-like $\underline{P}seudonocardia$ $\underline{P}olyene$ (NPP). The low productivity of NPP in P. autotrophica implies that its biosynthetic pathway is tightly regulated. In this study, $wblA_{pau}$ was isolated and identified as a novel negative regulatory gene for NPP production in P. autotrophica, which showed approximately 49% amino acid identity with a global antibiotic down-regulatory gene, wblA, identified from various Streptomycetes species. Although no significant difference in NPP production was observed between P. autotrophica harboring empty vector and the S. coelicolor wblA under its native promoter, approximately 12% less NPP was produced in P. autotrophica expressing the wblA gene under the strong constitutive $ermE^*$ promoter. Furthermore, disruption of the $wblA_{pau}$ gene from P. autotrophica resulted in an approximately 80% increase in NPP productivity. These results strongly suggest that identification and inactivation of the global antibiotic down-regulatory gene wblA ortholog are a critical strategy for improving secondary metabolite overproduction in not only Streptomyces but also non-Streptomyces rare actinomycete species.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.2
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• pp.116-120
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• 2006

We constructed four recombinant plasm ids to enhance the production of clavulanic acid (CA) in Streptomyces clavuligerus NRRL3585: (1) pIBRHL1, which includes ccaR, a pathway-specific regulatory gene involved in cephamycin C and CA biosynthesis; (2) pIBRHL2, containing claR, again a regulatory gene, which controls the late steps of CA biosynthesis; (3) pGIBR containing afsR-p, a global regulatory gene from Streptomyces peucetius; and (4) pKS, which harbors all of the genes (ccaR/ claR/ afsR-p). The plasmids were expressed in S. clavuligerus NRRL3585 along with the $ermE^*$ promoter. All of them enhanced the production of CA; 2.5-fold overproduction for pIBRHL1, 1.5-fold for pIBRHL2, 1.6-fold for pGIBR, and 1.5-fold for pKS compared to the wild type.

• Journal of Life Science
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• v.5 no.4
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• pp.162-169
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• 1995

The glpD genes encoding gly-3-p dehydrogenase is essential for the aerobic growth of E. coli on glycerol or gly-3-p. The glpE gene, the function of which is unknownm is transcribed divergently with respect to glpD gene. Expression of the adjacent but divergently transcribed glpD the glpE genes is positively regulated by the cAMP-CRP complex. In this study, for a precise investigation of the functional elements in the regulatory region for transcription activation by cAMP-CRP, deletion mutation have been introducted into the regulatory region. The effect of the deletion mutant on transcriptional regulation was tested in vivo by $\beta$-galctosidase activity. Deletion mutants in the regulatory region of glpD demonstrated that the presence of the CRP-binding site resulted in an sixfold increase in promoter activity. And also deletion mutants of glpE gene demonstrated that the presence of the CRP-binding site resulted in an eightfold increase in promoter activity. Insertion of 22 bp oligomer in the deletion mutants has shown that the CRP binding site is need for maximal expression of glpD and glpE genes. glpD and glpE gene, cAMP-CRP complex, deletion mutant, transcriptional regulation.