• Genomics & Informatics
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• 제5권3호
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• pp.129-132
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• 2007

arraylmpute is a software for exploratory analysis of missing data and imputation of missing values in microarray data. It also provides a comparative analysis of the imputed values obtained from various imputation methods. Thus, it allows the users to choose an appropriate imputation method for microarray data. It is built on R and provides a user-friendly graphical interface. Therefore, the users can easily use arraylmpute to explore, estimate missing data, and compare imputation methods for further analysis.

• Journal of Information Processing Systems
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• 제14권5호
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• pp.1167-1175
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• 2018

Microarray data plays an essential role in diagnosing and detecting cancer. Microarray analysis allows the examination of levels of gene expression in specific cell samples, where thousands of genes can be analyzed simultaneously. However, microarray data have very little sample data and high data dimensionality. Therefore, to classify microarray data, a dimensional reduction process is required. Dimensional reduction can eliminate redundancy of data; thus, features used in classification are features that only have a high correlation with their class. There are two types of dimensional reduction, namely feature selection and feature extraction. In this paper, we used k-means algorithm as the clustering approach for feature selection. The proposed approach can be used to categorize features that have the same characteristics in one cluster, so that redundancy in microarray data is removed. The result of clustering is ranked using the Relief algorithm such that the best scoring element for each cluster is obtained. All best elements of each cluster are selected and used as features in the classification process. Next, the Random Forest algorithm is used. Based on the simulation, the accuracy of the proposed approach for each dataset, namely Colon, Lung Cancer, and Prostate Tumor, achieved 85.87%, 98.9%, and 89% accuracy, respectively. The accuracy of the proposed approach is therefore higher than the approach using Random Forest without clustering.

• 한국정보과학회논문지:소프트웨어및응용
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• 제29권11호
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• pp.775-784
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• 2002

DNA chip 기술에 의해 얻어지는 마이크로어레이(microarray) 데이타는 세포나 조직 내의 수천 개 유전자의 발현도(expression level)를 한번에 측정한 것으로, 유전자 발현 양상에 기반한 암의 진단, 유전자의 기능 예측 등에 이용되고 있다. 다양한 데이타 분석 기법들 중 베이지안망(Bayesian network)은 데이타의 각 속성들간의 관계를 그래프 형태로 표현할 수 있는 특징을 가지고 있다. 이는 마이크로어레이 데이타의 분석을 통해 여러 유전자와 조직의 특성(암의 종류 등) 사이의 관계를 밝히는데 유용하다 하지만 대부분의 마이크로어레이 데이타는 sparse data로 베이지안망을 비롯한 각종 분석 기법의 적용을 어렵게 하고 있다. 본 논문에서는 베이지안망에 기반한 마이크로어레이 데이타 분석을 위해 효율적 구조 학습 알고리즘과 데이타 차원 축소를 이용한다. 제시되는 분석법은 실제 마이크로어레이 데이타인 NC160 data set에 적용되었으며, 그 유용성은 데이타로부터 학습된 베이지안망이 실제 생물학적으로 알려진 사실들을 어느 정도 정확하게 표현하는지에 의해 평가되었다.

• Molecules and Cells
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• 제25권2호
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• pp.279-288
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• 2008

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

• 한국통계학회:학술대회논문집
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• 한국통계학회 2005년도 추계 학술발표회 논문집
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• pp.37-41
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• 2005

Exploratory data analysis(EDA) is the initial stage of data analysis and provides a useful overview about the whole microarray experiment. If the experiments are replicated, the analyst should check the quality and reliability of microarray data within same experimental condition before the deeper statistical analysis. We shows EDA method focusing on the quality and reproducibility for replicates.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.30-36
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• 2006

Tissue microarray (TMA) is an array-based technology allowing the examination of hundreds of tissue samples on a single slide. To handle, exchange, and disseminate TMA data, we need standard representations of the methods used, of the data generated, and of the clinical and histopathological information related to TMA data analysis. This study aims to create a comprehensive data model with flexibility that supports diverse experimental designs and with expressivity and extensibility that enables an adequate and comprehensive description of new clinical and histopathological data elements. We designed a Tissue Microarray Object Model (TMA-OM). Both the Array Information and the Experimental Procedure models are created by referring to Microarray Gene Expression Object Model, Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE), and the TMA Data Exchange Specifications (TMA DES). The Clinical and Histopathological Information model is created by using CAP Cancer Protocols and National Cancer Institute Common Data Elements (NCI CDEs). MGED Ontology, UMLS and the terms extracted from CAP Cancer Protocols and NCI CDEs are used to create a controlled vocabulary for unambiguous annotation. We implemented a web-based application for TMA-OM, supporting data export in XML format conforming to the TMA DES or the DTD derived from TMA-OM. TMA-OM provides a comprehensive data model for storage, analysis and exchange of TMA data and facilitates model-level integration of other biological models.

• 제어로봇시스템학회논문지
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• 제11권10호
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• pp.830-836
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• 2005

Application of microarray technologies which monitor simultaneously the expression pattern of thousands of individual genes in different biological systems results in a tremendous increase of the amount of available gene expression data and have provided new insights into gene expression during drug development, within disease processes, and across species. There is a great need of data mining methods allowing straightforward interpretation, visualization and analysis of the relevant information contained in gene expression profiles. Specially, classifying biological samples into known classes or phenotypes is an important practical application for microarray gene expression profiles. Gene expression profiles obtained from tissue samples of patients thus allowcancer classification. In this research, molecular classification of microarray gene expression data is applied for multi-class cancer using computational biology such gene selection, principal component analysis and fuzzy clustering. The proposed method was applied to microarray data from leukemia patients; specifically, it was used to interpret the gene expression pattern and analyze the leukemia subtype whose expression profiles correlated with four cases of acute leukemia gene expression. A basic understanding of the microarray data analysis is also introduced.

• 응용통계연구
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• 제17권3호
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• pp.419-430
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• 2004

마이크로어레이 기술은 한번에 수만 개의 유전자를 동시에 분석할 수 있는 고효율, 고가의 새로운 연구 도구로 자리잡았으며 마이크로어레이 실험 자료의 올바른 분석을 위해서는 실험 목적에 맞는 실험계획법의 확립과 통계분석법의 적용이 중요하다 본 논문에서는 마이크로어레이 자료에서 여러 군 사이에서 발현의 차이를 보이는 유전자를 찾을 수 있는 되돌림 설계를 소개하고 ANOVA 모형을 이용하여 분석하는 방법을 제시한다. 연세대학교 암전이 연구센터의 되돌림 설계를 이용한 백혈병 자료를 MA-ANOVA(Wu et. al.(2003))를 이용하여 분석하였다

• 응용통계연구
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• 제22권1호
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• pp.89-106
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• 2009

There have been many new advances in the development of improved clustering methods for microarray data analysis, but traditional clustering methods are still often used in genomic data analysis, which maY be more due to their conceptual simplicity and their broad usability in commercial software packages than to their intrinsic merits. Thus, it is crucial to assess the performance of each existing method through a comprehensive comparative analysis so as to provide informed guidelines on choosing clustering methods. In this study, we investigated existing clustering methods applied to microarray data in various real scenarios. To this end, we focused on how the various methods differ, and why a particular method does not perform well. We applied both internal and external validation methods to the following eight clustering methods using various simulated data sets and real microarray data sets.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.29-34
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• 2005

DNA microarray becomes a major tool for the investigation of global gene expression in all aspects of cancer and biomedical research. DNA microarray experiment generates enormous amounts of data and they are meaningful only in the context of a detailed description of microarrays, biomaterials, and conditions under which they were generated. MicroArray Gene Expression Data (MGED) society has established microarray standard for structured management of these diverse and large amount data. MGED MAGE-OM (MicroArray Gene Expression Object Model) is an object oriented data model, which attempts to define standard objects for gene expression. To assess the relevance of DNA microarray analysis of cancer research it is required to combine clinical and genomics data. MAGE-OM, however, does not have an appropriate structure to describe clinical information of cancer. For systematic integration of gene expression and clinical data, we create a new model, Cancer Genomics Object Model.