• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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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.

• The KIPS Transactions:PartB
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• v.14B no.1 s.111
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• pp.33-42
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• 2007

This paper presents a new methodology for music structure analysis which facilitates rhetoric-based music summarization. Similarity analysis of musical constituents suggests the structure of a musical piece. We can recognize its musical form from the structure. Musical forms have rhetorical characteristics of their on. We have utilized the characteristics for locating musical motifs. Motif extraction is to music summarization what topic sentence extraction is to text summarization. We have evaluated the effectiveness of this methodology through a popular music case study.

• Journal of Plant Biotechnology
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• v.49 no.1
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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.

• Journal of fish pathology
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• v.32 no.2
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• pp.49-57
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• 2019

In this study, we collected 39 megalocytiviruses isolated from diseased fish in Korea from 2012 to 2018. Major capsid protein (MCP) gene, a part of vascular endothelial growth factor (VEGF) gene and histidine triad motif-like protein (HIT) genes of Megalocytivirus were targeted for PCR amplification and analysis of those DNA nucleotide sequences. Korean strains revealed two genotypes (red sea bream iridovirus and turbot reddish body iridovirus types) based on the phylogeny of MCP gene. The red sea bream iridovirus type (RSIV-type) megalocytiviruses were divided into RSIV-subgroup 1 and 2. From the phylogenetic analysis of the VEGF genes, a genotypic variant of RSIV-type Megalocytivirus was identified. The HIT-like protein gene was detected in RSIVs, but not in TBRIV and ISKNV, suggesting that HIT-like protein gene may be specific in RSIV.

• The Research Journal of the Costume Culture
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• v.15 no.2 s.67
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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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• v.29 no.2
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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.

• The Research Journal of the Costume Culture
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• v.4 no.1
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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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• v.45 no.5
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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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• v.2 no.2
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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.

• Analytical Science and Technology
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• v.24 no.6
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• pp.527-532
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• 2011

IQ motif-containing GTPase-activating protein 1 (IQGAP1), which is a well-known $Ca^{2+}$-independent calmodulin (CaM) binding protein, is involved in various cellular functions such as cell proliferation and cell migration. IQGAP1 has four repeated IQ motifs, which are crucial for CaM binding. It has been shown that all four IQ motifs of IQGAP1 can bind to $Ca^{2+}$/CaM, while the third and fourth IQ motifs of IQGAP1 can bind to apoCaM. However, it has not been clear whether the CaM binding of IQ motifs of IQGAP1 was mediated directly or indirectly. In this study, we examined whether the binding between CaM and each IQ motif of IQGAP1 was direct in vitro. As a result, we found that IQ1 motif has a weak $Ca^{2+}$-dependent CaM binding. In contrast, IQ3 has a $Ca^{2+}$-dependent CaM binding. All other motifs have no significant CaM binding. We also found that IQ(2.7-3) and IQ(3.5-4.4) have CaM binding capacity. This finding indicates that IQ motifs of IQGAP1 plays a dynamic role via different motif interactions with $Ca^{2+}$/CaM or proCaM.