• 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.

• 한국지능시스템학회논문지
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• 제17권5호
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• pp.707-711
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• 2007

Microarray gene expression data is believed to show the functions of living organism through the gene expression values. We have studied a method to get the informative genes from the microarray gene expression data. There are several ways for this. In recent researches to get more sophisticated and detailed results, it has used the intelligence information theory like fuzzy theory. Some methods are to add fudge factors to the significance test for more refined results. In this paper, we suggest a method to get informative genes from microarray gene expression data. We combined the difference of means between two groups and the fuzzy membership degree which reflects the variance of the gene expression data. We have called our significance test the Fuzzy Information method for Gene Expression data(FIGER). The FIGER calculates FIGER variation ratio and FIGER membership degree to show how strongly each object belongs to the each group and then it results in the significance degree of each gene. The FIGER is focused on the variation and distribution of the data set to adjust the significance level. Out simulation shows that the FIGER-test is an effective and useful significance test.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.139-152
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• 2002

Gene-shaving(Hastie et al, 2000) is a very useful method to identify a meaningful group of genes when the variation of expression is large. By shaving off the low-correlated genes with the leading principal component, the primary genes with the coherent expression pattern can be identified. Gene-shaving method works well If expression levels are varied enough, but it may not catch the meaningful cluster in low expression level or different expression time even with coherent patterns. The sliding window gene-shaving method which is to apply gene-shaving in each sliding window after hierarchical clustering is to compensate losing a meaningful set of genes whose variation is not large but distinct. The performance to identify expression patterns is compared for the simulated profile data by the different variance and expression level.

• Communications for Statistical Applications and Methods
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• 제12권2호
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• pp.335-348
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• 2005

The rapid development of microarray technologies enabled the monitoring of expression levels of thousands of genes simultaneously. Recently, the time course gene expression data are often measured to study dynamic biological systems and gene regulatory networks. For the data, biologists are attempting to group genes based on the temporal pattern of their expression levels. We apply the consensus clustering algorithm to a time course gene expression data in order to infer statistically meaningful information from the measurements. We evaluate each of consensus clustering and existing clustering methods with various validation measures. In this paper, we consider hierarchical clustering and Diana of existing methods, and consensus clustering with hierarchical clustering, Diana and mixed hierachical and Diana methods and evaluate their performances on a real micro array data set and two simulated data sets.

• Journal of Veterinary Science
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• 제24권3호
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• pp.40.1-40.6
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• 2023

Analysis of the VP1 gene sequence of the foot and mouth disease virus (FMDV) is critical to understanding viral evolution and disease epidemiology. A standard set of primers have been used for the detection and sequence analysis of the VP1 gene of FMDV directly from suspected clinical samples with limited success. The study validated VP1-specific degenerate primer-based reverse transcription polymerase chain reaction (RT-PCR) for the qualitative detection and sequencing of serotype O FMDV lineages circulating in India. The novel degenerate primer-based RT-PCR amplifying the VP1 gene can circumvent the genetic heterogeneity observed in viruses after cell culture adaptation and facilitate precise viral gene sequence analysis from clinical samples.

• Asian-Australasian Journal of Animal Sciences
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• 제16권10호
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• pp.1397-1401
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• 2003

The aim of this study was to determine genotypes of four genetic markers and to investigate their association with milk production traits in Brown Swiss cattle imported to Slovakia. The bovine $\kappa$-casein, $\beta$-lactoglobulin, growth hormone and prolactin genotypes of 107 cows were identified by polymerase chain reaction. Effects all four genetic markers on milk, fat, protein and lactose yields and fat, protein and lactose percentage were estimated from a data set of 249 lactations. The frequency of desirable B allele of $\kappa$-casein gene to milk production was 0.46, alleles A of $\beta$-lactoglobulin gene was 0.55, allele and L of growth hormone gene was 0.45 and allele A and B of bovine prolactin gene were 0.61 and 0.39. The results of milk production obtained in our work showed that BB genotypes of $\kappa$-CN gene, AA genotypes of $\beta$-LG gene, LL genotypes of bGH gene were significantly associated with better milk production traits, mainly about the fat content. Association of a bovine prolactin genotypes with milk production were not found.

• Journal of Crop Science and Biotechnology
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• 제11권3호
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• pp.157-162
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• 2008

A total of 2,765 accessions were used as the initial set having both seed coat color and 100-seed weight data. As a result of molecular profiling using six SSR markers followed by stratification based on their usages, 335 accessions(12.1%) were selected by clustering based on UPGMA. Since 75 out of 335 accessions were mixed in phenotypic traits as a result of characterization, 260 accessions were finally set as a core set. This core set revealed nearly the same diversity compared with the other results on morphological traits of Korean soybean landraces. In total, 115 alleles(19.2 alleles per locus) were detected in the initial set and 79 alleles(13.2 alleles per locus) were detected in the core set. All 30 major alleles were present in the initial set and in the core set as well. In allele coverage, the core set was 71.4% of the initial set. These comparisons of number of alleles, gene diversity and coverage indicated that the core set represented the entire set well.

• 생태와환경
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• 제40권1호
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• pp.149-154
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• 2007

남조류의 독성 잠재력을 확인하기 위해 microcystins 합성 유전자인 mcyB에 특이적으로 작용하는 TOX2P/TOX2M primer쌍을 이용한 whole-cell PCR을 실시하였다. 환경시료를 대상으로 한 실험 결과에서 TOX2P/TOX2M primer쌍은 약 1,000 $cells{\cdot}mL^{-1}$의 낮은 밀도에서 효과적으로 mcyB 유전자의 증폭에 성공하였으며, mcyB유전자를 지닌 종들은 모두 ELISA분석에 의해 microcystins의 생성이 확인되었다. 따라서, TOX2P/TOX2M primer쌍은 국내의 수체에서 독성 남조류의 신속하고 효과적인 검출을 위한 유용한 probe로 판단되었다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.275-275
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• 2022

One of the most widely grown food crops in the world, wheat, is increasing more lodged since for increased rains and winds caused by abnormal climate. During the Green Revolution, shorter wheat cultivars were bred using many Rht genes to increase lodging resistance. However, since only some Rht genes were used for breeding shorter wheat, it may have had a limited impact on wheat breeding and reduced genetic diversity. Therefore, it is essential to search for genes that have breeding potential and affect dwarfism in order to increase the genetic diversity of dwarf characteristics in wheat. In this study, we performed the RNA-seq between 'Keumkang' and 'Komac 5' ('Keumkang' mutant) to analyze the difference in plant height. Differentially expressed genes (DEGs) analysis and Gene function annotation were performed using 265,365,558 mapped reads. Cluster set analysis was performed to compress and select candidate gene DEGs affecting plant height, stem and internode. Gene expression analysis was performed in order to identify the functions of the selected genes by condensing the results of the DEG analysis into a cluster set analysis. This analysis of these plant height-related genes could help reduce plant height, improve lodging resistance, and increase wheat yield. Its application to wheat breeding will also affect the increased genetic diversity of wheat dwarfism.

• 생명과학회지
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• 제27권10호
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• pp.1104-1110
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• 2017

히스톤 H3K4의 메칠화는 3T3-L1의 지방세포의 분화를 촉진하는 것으로 알려져 있으나, 히스톤 H3K4 메칠화 효소인 SET1A가 지방세포 분화를 조절하는지에 대해서는 보고된 바가 없다. 그러므로 본 연구에서는 SET1A의 3T3-L1 지방세포의 분화조절과 기전을 연구하였다. SET1A의 발현은 3T3-L1 지방세포 분화과정에서 증가함을 관찰하였다. 3T3-L1 지방전구세포에서 siRNA을 이용하여 SET1A의 발현을 감소시키면 3T3-L1 지방전구세포의 분화가 억제됨을 관찰하여 SET1A가 3T3-L1 지방전구세포의 분화를 촉진함을 알 수 있었다. 이에 대한 조절기전을 알기 위해, SET1A의 발현을 감소시킨 3T3-L1 지방전구세포의 세포증식을 측정한 결과, 분화 초기 단계인 분화 후 2일 동안 3T3-L1 지방세포의 증식이 감소하였다. 또한 분화 후 7일 동안 지방세포세포 분화 조절인자들의 발현을 측정한 결과, SET1A의 발현을 감소시킨 3T3-L1 지방세포에서 $PPAR{\gamma}$의 발현이 감소하였다. 위와 같은 연구결과를 바탕으로, SET1A는 분화초기단계에서는 mitotic clonal expansion 단계를 촉진하고, 분화후기단계에서는 $PPAR{\gamma}$의 발현을 증가시켜 3T3-L1 지방세포의 분화를 촉진함을 알 수 있었다.