• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.63-68
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• 2005

Transcription factors regulate gene expression by binding to gene upstream region. Each transcription factor has the specific binding site in promoter region. So the analysis of gene upstream sequence is necessary for understanding regulatory mechanism of genes, under a plausible idea that assumption that DNA sequence motif profiles are closely related to gene expression behaviors of the corresponding genes. Here, we present an effective approach to the analysis of the relation between gene expression profiles and gene upstream sequences on the basis of kernel canonical correlation analysis (kernel CCA). Kernel CCA is a useful method for finding relationships underlying between two different data sets. In the application to a yeast cell cycle data set, it is shown that gene upstream sequence profile is closely related to gene expression patterns in terms of canonical correlation scores. By the further analysis of the contributing values or weights of sequence motifs in the construction of a pair of sequence motif profiles and expression profiles, we show that the proposed method can identify significant DNA sequence motifs involved with some specific gene expression patterns, including some well known motifs and those putative, in the process of the yeast cell cycle.

• 정보처리학회논문지B
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• 제14B권1호
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• pp.33-42
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• 2007

본 논문에서는 음악수사법에 기초하여 악곡요약을 구현할 새로운 악곡구조 분석 방법론을 소개한다. 이 방법론에서는 악곡 구성요소 간의 유사도 분석을 통해 악곡의 결합구조를 파악한 뒤, 결합구조에서 해당 곡이 취하고 있는 음악양식을 추정한다. 그 후 악식의 음악적 수사구조가 가지는 전통적인 특징과 표현기법을 근거로 악곡구조 안에서 주요선율을 추출한다. 문서요약의 경우와 같이 주어진 악보에서 추출된 주요선율은 그 곡의 요약이라고 간주할 수 있다. 개발한 악곡구조 분석 방법론은 대중음악 사례를 통하여 그 효용성을 가늠해 보았다.

• Journal of Plant Biotechnology
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• 제49권1호
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• pp.15-29
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• 2022

Cyclophilins (CYPs) are highly conserved ubiquitous proteins belong to the peptidyl prolyl cis/trans isomerase (PPIase) superfamily. These proteins are present in a wide range of organisms; they contain a highly conserved peptidyl-prolyl cis/trans isomerase domain. A comprehensive database survey identified a total of 35 genes localized in all cellular compartments of Solanum lycopersicum L., but largely in the cytosol. Sequence alignment and conserved motif analyses of the SlCYP proteins revealed a highly conserved CLD motif. Evolutionary analysis predicted the clustering of a large number of gene pairs with high sequence similarity. Expression analysis using the RNA-Seq data showed that the majority of the SlCYP genes were highly expressed in mature leaves and blooming flowers, compared with their expression in other organs. This study provides a basis for the functional characterization of individual CYP genes in the future to elucidate their role(s) in protein refolding and long-distance signaling in tomatoes and in plant biology, in general.

• 한국어병학회지
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• 제32권2호
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• pp.49-57
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• 2019

본 연구에서는 2012년부터 2018년 1월까지 국내 어류에서 참돔이리도바이러스병 (red sea bream iridoviral disease; RSIVD) 으로 확정 진단된 주요 분리주에 대하여 major capsid protein (MCP) 유전자의 염기서열을 바탕으로 Megalocytivirus의 유전적 관계를 명확히 했다. 또한, Megalocytivirus와 숙주 세포간 상호작용에 영향을 줄 수 있는 특이 유전자 2종, Vascular endothelial growth factor (VEGF) 및 Histidine triad motif인 HIT-like 단백질 (HIT)에 대한 염기서열 분석을 통해 유전적 상관관계를 고찰하였다. 국내 어류에서 분리된 39개의 megalocytiviruses는 2가지 유전형인 red sea bream iridovirus (RSIV)형과 turbot reddish body iridovirus (TRBIV)형으로 분류되었으며, RSIV형의 megalocytiviruses는 다시 유전아형인 RSIV-subgroup 1형과 2형으로 분류되었다. 그리고 VEGF 유전자 염기서열 분석 결과에서는 RSIV형의 바이러스에서 변이가 발생되었음을 확인할 수 있었으며, HIT-like 단백질 유전자는 RSIV형의 Megalocytivi rus에서만 발견되는 것을 알 수 있었다.

• 복식문화연구
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• 제15권2호
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• pp.193-202
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• 2007

The purpose of this study was to find out effects of textile motifs and the application methods on wearer's image perception. A survey was conducted to total of 255 male and female university students who are residing in Daejeon and Chungnam province. The stimuli were composed of 2 level tones(dark and light), 3 level complexity(simple, medial and complex), 3 patterns(polka dot, stripe and check) and the 2 way of stimuli application methods(fabric and garment). The instrument for measuring preference of stimuli consisted of 4 items, encouraging, preference, purchasing and popularity. The instrument for measuring image of stimuli consisted 24 pair items. Factor analysis for the adjective pair images(24 inquiries) about the textile patterns which were used in this study was performed. It resulted as three factors which are attraction, salience, and potential. Attraction, salience, and potency dimensions showed the most significant interaction effects of application methods and patterns. And tone and application method effected attraction and salience, tones and patterns effected attraction, tones and complex effected salience. Application methods and patterns effected potential and patterns and complex effected salience. The preferences toward stimuli, it resulted only interaction of tones and patterns affected the preferences('total preference' and 'purchasing'). Pearson's product-moment correlation analysis carried out to find out the relation of images of clothing and preferences. As a result, salience was significant relation with attraction and potency. In correlation between image of textile pattern and preference, attraction is most significant relation with the preference. The results of the study could be used for the marketing strategies of the motif in fashion product.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.381-388
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• 2008

An X-linked skeletal disorder, SEDT (spondyloepiphyseal dysplasia tarda) is a genetic disease characterized by a disproportionately short trunk and short stature caused by mutations in the SEDL gene. This gene is evolutionarily conserved from yeast to human. The yeast SEDL protein ortholog, Trs20p, has been isolated as a member of a large multi-protein complex called the transport protein particle (TRAPP), which is involved in endoplasmic reticulum (ER)-to-Golgi transport. The interaction between SEDL and partner proteins is important in order to understand the molecular mechanism of SEDL functions. We isolated several SEDL-binding proteins derived from rat cells by an immobilized GST-fusion method. Furthermore, the SEDL-homologue proteins were identified using motif based methods. Common motifs between SEDL-binding proteins and SEDL-homologue proteins were classified into seven types and 78 common motifs were revealed. Sequence similarities were contracted to seven types using phylogenetic trees. In general, types I-III and VI were classified as having the function of acetyl-CoA carboxylase, glycogen phosphorylase, isocitrate dehydrogenase, and enolase, respectively, and type IV was found to be functionally related to the GST protein. Types V and VII were found to contribute to TRAPP vesicle trafficking.

• 복식문화연구
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• 제4권1호
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• pp.57-74
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• 1996

The elderly population of Korea has been significantly increasing due to advances in public health, medical care, and quality of life. Social and economic influence of the elderly population has been also increasing. A elderly people become more interested in their appearance and clothing than before, clothing plays an important role in the elderly women's everyday life. The objectives of the research are to explore the life satisfaction, appearance satisfaction, clothing satisfaction, and clothing design preference of 416 women aged 55 years and older were residents of Seoul. Data were gathered through survey using a self-administered questionnaire from November, 1994 to January, 1995 in 8 senior schools and 3 senior centers which were scattered in Seoul. Descriptive statistics, t-test, and factor analysis were used in analysing the data. The results of this study indicated that life satisfaction have a positive relationship with clothing satisfaction. The respondents were divided into tow groups by life satisfaction. The higher life satisfaction group preferred skits and formal wear to the lower. But, two groups did not show any significant differences in terms of the colo preference, motif preference, and fabric preference. The result of factor analysis divided appearance satisfaction into body satisfaction and face satisfaction. Body satisfaction had a positive relationship with clothing satisfaction. And the group of lower physical satisfaction showed lower satisfaction in apparel fitness. Also the face satisfaction had a positive relationship with clothing satisfaction. The group of higher physical satisfaction preferred skirts and foraaml wear compared to that of lower physical satisfaction. The color preference and motif preference between two groups showed no significant difference. And the group of higher physical satisfaction preferred fabric that enhances the clothing style. Also, the group of higher ace satisfaction preferred fabric that enhances the clothing style. However, there was no significant difference in the color preference and motif preference between tow groups. The findings of this study amy contribute to knowledge about clothing satisfaction and preference of elderly women in Seoul since there have been few studies, and be useful to apparel manufacturers as well s clothing researchers. Also, research subjects of this study could be extended to aged men and various regions.

• Molecules and Cells
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• 제45권5호
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• pp.343-352
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• 2022

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the gene-regulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

• Bioinformatics and Biosystems
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• 제2권2호
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• pp.52-57
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• 2007

The computational discovery of transcription factor binding site is one of the important tools in the genetic and genomic analysis. Rough prediction of gene regulation network and finding possible co-regulated genes are typical applications of the technique. Countless motif-discovery algorithms have been proposed for the past years. However, there is no dominant algorithm yet. Each algorithm does not give enough accuracy without extensive information. In this paper, we explore the possibility of combining multiple algorithms for the one integrated result in order to improve the performance and the convenience of researchers. Moreover, we apply new high order information that is reorganized from the set of basis predictions to the final prediction.

• 분석과학
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• 제24권6호
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• pp.527-532
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• 2011

IQGAP1은 세포 내에서 암세포화, 세포이동과 같은 다양한 기능을 수행하고 있으며, $Ca^{2+}$-비의존성 calmodulin (CaM) 결합 단백질로 잘 알려져 있다. IQGAP1내에는 IQ부위가 4 번 반복해서 나타나는데, 이 부위가 IQGAP1의 CaM 결합에 중요한 역할을 한다고 알려져 있다. 이전의 연구를 통해 4개의 IQ 부위 모두 $Ca^{2+}$/CaM과의 결합에 관여하고, IQ3와 IQ4는 $Ca^{2+}$이 결합되지 않는 상태의 CaM인 proCaM 결합에 관여 한다고 알려져 있다. 그러나, 이러한 각각의 IQ 부위와의 결합성이 CaM과 직접적인 결합인지, 아니면 다른 단백질이 매개하는 간접적인 결합인지 알려져 있지 않았다. 따라서, 본 연구에서는 IQGAP1의 각각의 IQ 부위와 CaM의 결합성을 직접적으로 알아보기 의해 in vitro에서 조사해 보았다. 그 결과, 흥미롭게도 이전의 결과와는 다르게 4개의 IQ 부위 중에서 IQ3는 의미있는 $Ca^{2+}$-비의존성 CaM결합성이 있음을 알게 되었고, IQ1는 약한 $Ca^{2+}$-의존성 CaM 결합성이 있음을 알게 되었다. 반면에, 다른 IQ 부위들은 CaM과의 결합력이 약하거나 없음을 확인하였다. 또한, 기존의 IQ 부위 이외에 IQ(2.7-3)과 IQ(3.5-4.4) 부위가 의미있는 CaM 결합성이 있음을 확인하게 되었다. 따라서, 본 연구 결과 CaM이 IQGAP1을 기존의 보고와는 다른 방식으로 조절할 수 있을 가능성이 있음을 알게 되었고, 새로운 결합 부위 동정을 통해 IQGAP1과 CaM의 결합이 미치는 생리학적인 의미를 연구할 수 있는 토대를 마련하였다.