• Genomics & Informatics
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• 제16권4호
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• pp.38.1-38.3
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• 2018

Gene-gene interaction (GGI) analysis is known to play an important role in explaining missing heritability. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in a case-control design. In this study, we developed "Hierarchical structural CoMponent analysis of Gene-Gene Interactions" (HisCoM-GGI) software for GGI analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and single nucleotide polymorphisms (SNPs), enabling both gene-level and SNP-level interaction analysis in a single model. Furthermore, this software accepts various types of genomic data and supports data management and multithreading to improve the efficiency of genome-wide association study data analysis. We expect that HisCoM-GGI software will provide advanced accessibility to researchers in genetic interaction studies and a more effective way to understand biological mechanisms of complex diseases.

• Genomics & Informatics
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• 제11권3호
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• pp.135-141
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• 2013

Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait ($p_{corr}$ < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

• Genomics & Informatics
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• 제18권4호
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• pp.38.1-38.9
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• 2020

Chronotype is an important moderator of psychiatric illnesses, which seems to be controlled in some part by genetic factors. Clock genes are the most relevant genes for chronotype. In addition to the roles of individual genes, gene-gene interactions of clock genes substantially contribute to chronotype. We investigated genetic associations and gene-gene interactions of the clock genes BHLHB2, CLOCK, CSNK1E, NR1D1, PER1, PER2, PER3, and TIMELESS for chronotype in 1,293 healthy Korean individuals. Regression analysis was conducted to find associations between single nucleotide polymorphism (SNP) and chronotype. For gene-gene interaction analyses, the quantitative multifactor dimensionality reduction (QMDR) method, a nonparametric model-free method for quantitative phenotypes, were performed. No individual SNP or haplotype showed a significant association with chronotype by both regression analysis and single-locus model of QMDR. QMDR analysis identified NR1D1 rs2314339 and TIMELESS rs4630333 as the best SNP pairs among two-locus interaction models associated with chronotype (cross-validation consistency [CVC] = 8/10, p = 0.041). For the three-locus interaction model, the SNP combination of NR1D1 rs2314339, TIMELESS rs4630333, and PER3 rs228669 showed the best results (CVC = 4/10, p < 0.001). However, because the mean differences between genotype combinations were minor, the clinical roles of clock gene interactions are unlikely to be critical.

• KSBB Journal
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• 제8권2호
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• pp.104-109
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• 1993

한 개의 pladsmid에 Gus gene과 Hygromycin resistant gene(Hpt)을 합친 vector를 개발하였다. 이 재조합된 DNA를 벼의 건조한 종자에 imbibition시켜 형질전환했을 때, hygromycin 배지에서 선별한 결과 그 발현율은 single Hpt vector와 차이 가 없었으며, 주로 뿌리의 생장점이나 자엽초에서 Gus expression을 볼 수 있였다. 또한 hygromycin 배지에서 선별되어 성체가 된 개체에서 그 genomic DNA를 뽑아 PCR을 한 결과 1Kb Hpt gene을 확인하였다. 그리고 생체에서 추출한 총 RNA에서 cDNA를 만든 후 reverse transcription PCR을 통하여, 외부 유전자의 발현을 증명하였다.

• 한국어병학회지
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• 제34권2호
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• pp.177-184
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• 2021

Vaccines based on single-cycle viruses that are replication-incompetent due to knockout of replication-related structural gene(s) are more immunogenic than inactivated or subunit vaccines and can be used as delivery vehicles for foreign antigens without concerns on the reverting to virulent forms. The aim of this study was to develop a delivery vehicle for nervous necrosis virus (NNV)-like particles (VLPs) using G gene deleted single-cycle VHSV (rVHSV-𝚫G). Recombinant single-cycle VHSVs carrying NNV capsid protein gene between N and P gene of rVHSV-𝚫G genome (rVHSV-𝚫G-NNV_Cap) were rescued by reverse genetic technology. The successful expression of NNV capsid protein in cells infected with rVHSV-𝚫G-NNV_Cap was demonstrated by Western blot analysis, and the production of NNV VLPs in infected cells was confirmed using an electron microscopy. The results suggest that single-cycle VHSVs can be used as a safe delivery vehicle for NNV VLPs, and can be extended to other pathogens for the development of prophylactic vaccines.

• 한국육종학회지
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• 제42권1호
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• pp.23-27
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• 2010

The objective of this study was to map the gene for reduced embryo size in rice using DNA markers. The reduced embryo size mutant was induced from N-methyl-N-nitrosourea (MNU) treated Taichung 65. Genetic analysis revealed that the phenotype of the reduced embryo was controlled by a single recessive gene, designated as re-1. For mapping the gene controlling embryo size, an $F_2$ population was developed from a cross between the Korean Tongil-type, Milyang 23 (Oryza sativa ssp. indica) and the mutant. The ratio of $F_2$ seeds nearly fitted to 3:1 ratio, indicating that this phenotype was controlled by a single recessive gene. Bulked sergeant analysis was performed with SSR markers. The gene for the reduced embryo size was detected on chromosome 1. The gene was further mapped between two SSR markers, RM315 and RM265 on chromosome 1 (approximately 1.5 Mb interval). The linked markers will facilitate selection of this grain character in a breeding program and provide the foundation for positional cloning of this gene.

• Animal cells and systems
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• 제7권2호
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• pp.159-164
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• 2003

The RAD3 gene of Saccharomyces cerevisiae is required for excision repair and is essential for cell viability. The RAD3 encoded protein possesses a single stranded DNA-dependent ATPase and DNA and DNA-RNA helicase activities. To examine the extent of conservation of structure and function of a S. pombe RAD3 during eukaryotic evolution, the RAD3 homolog gene was isolated by screening of genomic DNA library. The isolated gene was designated as HRD3 (homolog of RAD3 gene). Southern blot analysis confirmed that S. pombe chromosome contains the same DNA as HRD3 gene and this gene exists as a single copy in S. pombe. The transcript of 2.8 kb was detected by Northern blot analysis, The level of transcripts increased by ultraviolet (UV) irradiation, indicating that HRD3 is one of the UV-inducible genes in S. pombe. Furthermore, the predicted partial sequence of HRD3 protein has 60％ identity to S. cerevisiae RAD3 gene. This homology was particularly striking in the regions identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that the HRD3 gene is essential for viability and DNA repair function. These observations suggest evolutionary conservation of other protein components with which HRD3 might interact in mediating its DNA repair and viability functions.

• 한국가축번식학회지
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• 제27권3호
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• pp.225-231
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• 2003

본 연구는 생체 내 세포 및 조직배양기로서의 면역결핍동물을 개발할 목적으로 proximal lck promoter와 DT-A gene를 이용하여 형질전환생쥐을 생산하고 이 형질전환생쥐의 면역세포에서 DT-A gene이 발현되는지를 분석하였다. 형질전환생쥐와 정상생쥐로부터 thymus, spleen 및 liver에서 RNA를 추출하여 RT-PCR수행하였는데 정상생쥐의 조직에서는 어떠한 DT-A gene의 발현양상을 얻을 수 없었으나 형질전환생쥐의 thymus, spleen, liver에 DT gene의 발현을 확인할 수 있었고, Northern blotting을 이용하여 형질전환생쥐의 thymus, spleen 및 liver에서 DT-A gene이 강하게 발현되는 것으로 나타났다. 형질전환생쥐 $F_1$ 및 $F_2$ 산자의 혈액에서 T-cell 발달의 분포도를 확인하기 위해 CD4 및 CD8 antibody를 이용하여 FACS analysis를 실시하였는데 형질전환생쥐의 혈액 내 mature T-cell인 single positive thymocyte의 수가 정상생쥐에 비해 감소하는 경향을 나타냈다. 정상생쥐의 혈액 내 T-cell 중 $CD8^{+}$ T-cell의 경우 약 50%를 나타냈으나 형질전환생쥐의 경우 33%로 감소하였고, $CD4^{+}$ T-cell은 정상생쥐에서 10%를 차지하고 있으나 형질전환생쥐에서는 5.9%로 감소되는 것으로 분석되었다. 그러므로 본 연구의 형질전환생쥐에서 lck promoter에 의해 초기 immature한 상태의 T-cell에서 DT-A gene이 발현되어 발육중인 T-cell이 파괴 되어 mature 상태인 $CD4^{+}CD8^{-}$나 $CD4^{-}CD8^{+}$ cells (single-positive)들이 감소된 것으로 확인되었다.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2005년도 창립 30주년 및 춘계학술대회
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• pp.18-18
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• 2005

• Communications for Statistical Applications and Methods
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• 제16권3호
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• pp.397-408
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• 2009

마이크로어레이 기술은 수만 개 유전자의 발현 패턴을 동시에 관찰하는 것을 가능하게 하였고, 이들을 하나씩 검정하여 찾아낸 특이발현 현상을 보이는 유전자를 중심으로 질병의 진단, 치료법 정립과 신약 개발을 위한 기본 정보를 확립하였다. 그러나 개별 유전자분석의 여러 문제점이 발견되면서 유전자들을 생물학적 대사경로나 염색체 위치가 같은 것끼리 묶은 집단을 분석하여 질병의 발생이나 생존에 영향을 미치는 집단을 찾는 방법이 제시되었다. 이러한 유전자 집단의 유의성에 대한 연구는 2002년에 MIT에서 비롯되어 GSEA, SAM-GS와 중심극한 정리의 개념을 이용한 모수적 방법인 PAGE 등이 사용되고 있다. 본 논문에서는 이들 통계량의 구조적 한계를 극복하고 계산이 간단한 새로운 모수적 방법을 제안하고 자료 분석을 통하여 효율성을 보였다.