• Journal of the Korean Data and Information Science Society
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• 제18권4호
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• pp.1005-1021
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• 2007

Traditional procedures for DNA microarray data analysis are to preprocess and normalize the gene expression data, and then to analyze the normalized data using statistical tests. Drawbacks of the traditional methods are: genuine biological signal may be unwillingly eliminated together with artifacts, the limited number of arrays per gene make statistical tests difficult to use the normality assumption or nonparametric method, and genes are tested independently without consideration of interrelationships among genes. A novel method using average rank in each array is proposed to eliminate such drawbacks. This average rank method monitors differentially regulated genes among genetically different groups and the selected genes are somewhat different from those selected by traditional P-value method. Addition of genes selected by the average rank method to the traditional method will provide better understanding of genetic differences of groups.

• 한국미생물·생명공학회지
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• 제23권2호
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• pp.123-130
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• 1995

DNA topoisomerase I have been shown to be important therapeutic target in cancer chemotherapy. Chemotaxonomy and numerical identification were carried out for an isolate strain No.7489 producing an antibiotic that inhibits DNA topoisomerase I activity. The genus of strain No.7489 was determined as Streptomyces sp. from culture, morphological and chemotaxonomic data. Thirty-nine taxonomic unit characters were tested and the data were analyzed numerically using the TAXON program. The isolate was best matched to Streptomyces melanosporofaciens in the major cluster 32 of Streptomyces. Therefore, it was concluded that the isolate was identified to be a member of Streptomyces melanosporofaciens.

• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 2000년도 춘계학술대회 학술발표 논문집
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• pp.224-227
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• 2000

In this Paper, we prepose a method of constructing neural networks using bio-inspired emergent and evolutionary concepts. This method is algorithm that is based on the characteristics of the biological DNA and growth of plants. Here is, we propose a constructing method to make a DNA coding method for production rule of L-system. L-system is based on so-called the parallel rewriting mechanism. The DNA coding method has no limitation in expressing the production rule of L-system. Evolutionary algorithms motivated by Darwinian natural selection are population based searching methods and the high performance of which is highly dependent on the representation of solution space. In order to verify the effectiveness of our scheme, we apply it to one step ahead prediction of Mackey-Glass time series, Sun spot data and KOSPI data.

• 응용통계연구
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• 제18권1호
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• pp.115-127
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• 2005

DNA마이크로어레이 기술은 수천 개 또는 수만 개의 유전자의 발현을 동시에 탐색할 수 있는 새로운 과학 기술이다. 표준화(normalization)는 마이크로어레이 실험에서 다양한 원인에 의해 발생하는 잡음(noise)을 줄이거나 제거하는 과정을 나타낸다. print-tip의 변동은 잡음의 주요 요인으로 인지되어 왔다. 본 논문에서는 잡음의 주요 발생요인이 되는 print-tip의 변동을 조절하기 위한 print-tip 표준화 작업에 대한 객관적인 비교 및 그 타당성 평가를 하였다. 먼저 그동안 제안된 여러 표준화 방법들 중에서 가장 널리 사용되고 있는 방법들을 정리해서 소개한 후에, 잡음이 많이 포함된 실제 cDNA 실험자료를 이용하여 각 표준화 방법의 특성을 비교해 보았다. 또한 실험자료와 유사한 모의분포를 생성한 후에 print-tip 표준화 작업에 대한 체계적인 비교를 해 보았다.

• 한국미생물·생명공학회지
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• 제38권1호
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• pp.70-76
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• 2010

The single-stranded large circular (LC)-sense DNA were utilized as probes for DNA chip experiments. The microarray experiment using LC-sense DNA probes found differentially expressed genes in A549 cells as compared to WI38VA13 cells, and microarray data were well-correlated with data acquired from quantitative real-time RT-PCR. A 5K LC-sense DNA microarray was prepared, and the repeated experiments and dye swap test showed consistent expression patterns. Subsequent functional analysis using LC-antisense library of overexpressed genes identified several genes involved in A549 cell growth. These experiments demonstrated proper feature of LC-sense molecules as probe DNA for microarray and the potential utility of the combination of LC-sense microarray and antisense libraries for an effective functional validation of genes.

• 약학회지
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• 제49권6호
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• pp.484-489
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• 2005

Streptococcus pmeumoniae is the leading cause of pneumonia and bacterial meningitis. The current polysaccharide vaccine has been reported ineffective in elderly adults and children less than 2 years of age. Thus, in recent many researchers have been focused on a different approach, DNA vaccine. In our laboratory we developed a Streptococcus pneumoniae DNA (SPDNA) vaccine. This SPDNA vaccine was formulated by inserting the region encoding part of the capsule in the S. pneumoniae into the LAMP-1. In present work, with use of the SPDNA vaccine we attempted to establish a certain methodology useful for evaluation of effectiveness and immunoresponse of a DNA vaccine. Results showed that the subcutaneous route was the most effective for production of antisera specific for S. pneumoniae in mice. By isotyping analyses, IgM, IgGl, IgG2a, and IgG2b were determined. In addition, INF-$\gamma$ and IL-4 were predominantly detected. Combination of those data resulted in a pattern of IgGl < IgG2a=IgG2b and INF$\gamma\>$ >IL-4, which indicates the inmmunity towards the Thl response predominantly; furthermore, the SPDNA vaccination induced resistance of the CD4+T lymphocyte-depleted mice against disseminated pneumococcal infection. These data appear to be possibly due to activation of CDS8+T cell-activation. Taken together, this methodology can be applied for evaluating efficacy and mode of action of a DNA vaccine as minimum critera.

• Plant Resources
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• 제3권3호
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• pp.211-218
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• 2000

Intraspecific genetic relationship of 19 variation types of the Yam (Dioscorea alata) classified by their external morphological characteristics such as leaf and tuber shape were assessed by DNA using random and specific primer. Twenty two out of 113 primers (100 random[10-mer] primers, two 15 mer [M13 core sequence, and (GGAT)$_4$ sequence]) had been used in PCR-amplification. Only 12 primers, however, were success in DNA amplification in all of the analyzed plants, resulting in 93 randomly and specifically amplified DNA fragments. The analyzed taxa showed very high polymorphisms(69 bands, 71.0 %), allowing individual taxon to be identified based on DNA fingerprinting. Monomorphic bands among total amplified DNA bands of each primer was low under the 50%. Similarity indices between accessions were computed from PCR(polymerase chain reaction) data, and genetic relationships among intraspecific variations were closely related at the levels ranging from 0.66 to 0.90. These DNA data were not matched well with those of morphological characters since they were divided into two major groups at the similarity coefficient value of 0.70. Therefore, Grouping of species into variation types by mainly morphological charactistics was suggested unreasonable.

• International Journal of Computer Science & Network Security
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• 제21권8호
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• pp.281-287
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• 2021

Bioinformatics is formed with a blend of biology and informatics technologies and it employs the statistical methods and approaches for attending the concerning issues in the domains of nutrition, medical research and towards reviewing the living environment. The ceaseless growth of DNA sequencing technologies has resulted in the production of voluminous genomic data especially the DNA sequences thus calling out for increased storage and bandwidth. As of now, the bioinformatics confronts the major hurdle of management, interpretation and accurately preserving of this hefty information. Compression tends to be a beacon of hope towards resolving the aforementioned issues. Keeping the storage efficiently, a methodology has been recommended which for attending the same. In addition, there is introduction of a competent algorithm that aids in exact matching of small pattern. The DNA representation sequence is then implemented subsequently for determining 2 bases to 6 bases matching with the remaining input sequence. This process involves transforming of DNA sequence into an ASCII symbols in the first level and compress by using LZ77 compression method in the second level and after that form the grid variables with size 3 to hold the 100 characters. In the third level of compression, the compressed output is in the grid variables. Hence, the proposed algorithm S_Pattern DNA gives an average better compression ratio of 93% when compared to the existing compression algorithms for the datasets from the UCI repository.

• Journal of the Korean Data and Information Science Society
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• 제14권4호
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• pp.759-772
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• 2003

K-Means and Web mining modelling have been tried for finding major DNA marker of BM4311 microsatellite loci in Hanwoo Chromosome 6 linkage map. Furthermore, a major DNA mining by bootstrap simulations(BCa) has been applied.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.97-115
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• 2001

cDNA microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. Many statistical analysis tools become widely applicable to the analysis of cDNA microarray data. In this talk, we consider a two-way ANOVA model to differentiate genes that have high variability and ones that do not. Using this model, we detect genes that have different gene expression profiles among experimental groups. The two-way ANOVA model is illustrated using cDNA microarrays of 3,800 genes obtained in an experiment to search for changes in gene expression profiles during neuronal differentiation of cortical stem cells.