• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2007.04a
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• pp.237-240
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• 2007

본 논문에서는 유전자 발현데이터로부터 유전자 조절네트워크를 추론하는 유전자 알고리즘을 제안한다. 근래에 유전자 알고리즘을 이용하여 유전자 조절네트워크를 추론하려는 시도가 있었으나 그리 성공적이지 못하였다. 우리는 본 논문에서 유전자 조절네트워크를 보다 효율적으로 추론할 수 있게 하기 위하여 새로운 유전자 인코딩 기법을 개발하여 적용하였다. 선형 유전자 조절네트워크로 모델링 된 인공 유전자 조절네트워크를 사용하여 실험한 결과 대부분의 경우에 있어서 주어진 인공 유전자 조절네트워크와 유사한 네트워크를 추론하였으며 완전히 동일한 유전자네트워크를 추론하기도 하였다. 향후 실제 유전자 발현 데이터를 이용하여 추론해 보는 것이 필요하다.

• Korean Journal of Veterinary Research
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• v.52 no.3
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• pp.183-191
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• 2012

The maintenance of peripheral immune tolerance and prevention of chronic inflammation and autoimmune disease require $CD4^{+}CD25^{+}$ T cells (regulatory T cells). The transcription factor Foxp3 is essential for the development of functional, regulatory T cells, which plays a prominent role in self-tolerance. Retroviral vectors can confer high level of gene transfer and transgene expression in a variety of cell types. Here we observed that following retroviral vector-mediated gene transfer of Foxp3, transductional Foxp3 expression was increased in the liver, lung, brain, heart, muscle, spinal cord, kidney and spleen. One day after vector administration, high levels of transgene and gene expression were observed in liver and lung. At 2 days after injection, transductional Foxp3 expression level was increased in brain, heart, muscle and spinal cord, but kidney and spleen exhibited a consistent low level. This finding was inconsistent with the increase in both $CD4^{+}CD25^{+}$ T cell and $CD4^{+}Foxp3^{+}$ T cell frequencies observed in peripheral immune cells by fluorescence-activated cell-sorting (FACS) analysis. Retroviral vector-mediated gene transfer of Foxp3 did not lead to increased numbers of $CD4^{+}CD25^{+}$ T cell and $CD4^{+}Foxp3^{+}$ T cell. These results demonstrate the level and duration of transductional Foxp3 gene expression in various tissues. A better understanding of Foxp3 regulation can be useful in dissecting the cause of regulatory T cells dysfunction in several autoimmune diseases and raise the possibility of enhancing suppressive functions of regulatory T cells for therapeutic purposes.

• Fisheries and Aquatic Sciences
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• v.15 no.4
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• pp.317-324
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• 2012

We characterized the cytoskeletal beta-actin (${\beta}$-ACT) gene (actb) and its 5'-upstream regulatory region in the Javanese ricefish Oryzias javanicus. The gene and protein structures were deduced from amino acid sequences of the actb gene and conserved in the teleost lineage. The O. javanicus actb gene has common transcription factor binding motifs in its regulatory region found in teleostean orthologues. Following quantitative reverse transcription-PCR, actb gene transcripts were detected in all tissues examined; however, the basal expression levels were different. During early development, O. javanicus actb mRNA levels showed a gradual increase and peaked between late somitogenesis and the heartbeat stage. Microinjection of O. javanicus embryos with the actb gene promoter-driven red fluorescent protein (RFP) gene reporter vector showed a ubiquitous distribution of RFP signals, although most exhibited a mosaic pattern of transgene expression. A small number of microinjected embryos displayed a wide distribution of RFP signals over their entire body, which resembled the expression pattern of endogenous actb. Data from this study provide a basis to develop a transgenic system with ubiquitous expression of foreign genes in O. javanicus.

• Animal cells and systems
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• v.9 no.3
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• pp.107-111
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• 2005

C. elegans DLK-1 has been reported to play an important role in synaptogenesis by shaping the structure of presynaptic terminal. In this study, we investigated the expression pattern and regulation of the dlk-1 gene in C. elegans. To determine the expression pattern, we made a dlk-1::gfp fusion construct, named pPDdg1, which consisted of -2.2 kb 5' upstream region, the first exon, the first intron, and a part of the second exon of the dlk-1 gene. By microinjecting this construct into the worm, we observed that the DLK-1::GFP was expressed mainly in neurons. We next examined the regulatory elements of gene expression by deletion analysis of pPDdg1. Removal of a large portion of the 5' upstream region (${\Delta}-361$ to -2246) of the gene had little effect on the expression pattern, whereas deletion of the first intron led to elimination of the DLK-1::GFP expression in most of the neurons. Our results suggest that the first intron of the C. elegans dlk-1 gene contains the regulatory element critical for gene expression.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.4
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• pp.2265-2268
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• 2013

Several lines of evidence indicate that cancer is a multistep process. To survey the mechanisms involving gene alteration and miRNAs in adrenocortical cancer, we focused on transcriptional factors as a point of penetration to build a regulatory network. We derived three level networks: differentially expressed; related; and global. A topology network ws then set up for development of adrenocortical cancer. In this network, we found that some pathways with differentially expressed elements (genetic and miRNA) showed some self-adaption relations, such as EGFR. The differentially expressed elements partially uncovered mechanistic changes for adrenocortical cancer which should guide medical researchers to further achieve pertinent research.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.339-343
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• 2005

Boolean networks(BN) construction is one of the commonly used methods for building gene networks from time series microarray data. However, BN has two major drawbacks. First, it requires heavy computing times. Second, the binary transformation of the microarray data may cause a loss of information. This paper propose two methods using liner regression to construct gene regulatory networks. The first proposed method uses regression based BN variable selection method, which reduces the computing time significantly in the BN construction. The second method is the regression based network method that can flexibly incorporate the interaction of the genes using continuous gene expression data. We construct the network structure from the simulated data to compare the computing times between Boolean networks and the proposed method. The regression based network method is evaluated using a microarray data of cell cycle in Caulobacter crescentus.

• YAKHAK HOEJI
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• v.37 no.5
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• pp.504-510
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• 1993

Human insulin gene is consisted of the polymorphic region with the repeating units, the regulatory sequence, the structural gene including the intervening sequence, and 3'-flanking region. The polymerase chain reaction, which amplifies the target DNA between two specific primers, has been performed for the amplification of human insulin gene and simple one-step cloning of it into Escherichia coli. Out of 1727 nuceotides compared, only 4 sites were variable: 5'-regulatory region(G2101$\rightarrow$AGG); IVS I(T2401$\rightarrow$A); Exon II(C2411 deletion); IVS II(A2740 dejection). The variations at the G2101 and T2401 were the same as those found in one American allele. The other two variations were observed only in the specific Korean allele. And, the enzyme digestion patterns among normal, insulin dependent diabetes mellitus, and non-insulin dependent diabetes mellitus were the same. On the other hand, PCR method showed the possibility of the quickaccess for the polymorphic region in terms of the restriction fragment length of polymorphism.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1995.10a
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• pp.9-15
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• 1995

When quiescent cells ate stimulated to enter the cell cycle, the thymidine kinase(TK) gene is transcriptionally activated at the border of Gl and 5. In this report we show that the human TK promoter contains multiple protein-binding sites. By site-directed mutagenesis, we identified a protein-binding site on the human TK promoter requited for conferring Gl-S-regulated transcription to a heterologous promoter and dissociated it functionally from an adjacent protein-binding domain containing an inverted CCAAT motif requited for high basal level expression. Substitution-mutation of this site results in constitutive expression of the neo reporter gene in serum-stimulated fibroblasts, as well as in cells arrested in mid-Gl by a temperature-sensitive mutation. The regulatory domains for the human TK promoter exhibit interesting symmetrical features, including a set of CCAAT motifs and sites similar to the novel Yi protein-binding site recently discovered in the mouse TK promoter. Thus, components of the hTK complex is important for hTK gene regulation.

• Genomics & Informatics
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• v.13 no.2
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• pp.40-44
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• 2015

DNA microarray and next-generation sequencing provide data that can be used for the genetic analysis of multiple quantitative traits such as gene expression levels, transcription factor binding profiles, and epigenetic signatures. In particular, chromatin opening is tightly coupled with gene transcription. To understand how these two processes are genetically regulated and associated with each other, we examined the changes of chromatin accessibility and gene expression in response to genetic variation by means of quantitative trait loci mapping. Regulatory patterns commonly observed in yeast and human across different technical platforms and experimental designs suggest a higher genetic complexity of transcription regulation in contrast to a more robust genetic architecture of chromatin regulation.

• Genomics & Informatics
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• v.11 no.4
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• pp.200-210
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• 2013

Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.