• Genomics & Informatics
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• v.9 no.1
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• pp.19-27
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• 2011

Gene Expression Omnibus (GEO) has kept the largest amount of gene-expression microarray data that have grown exponentially. Microarray data in GEO have been generated in many different formats and often lack standardized annotation and documentation. It is hard to know if preprocessing has been applied to a dataset or not and in what way. Standard-based integration of heterogeneous data formats and metadata is necessary for comprehensive data query, analysis and mining. We attempted to integrate the heterogeneous microarray data in GEO based on Minimum Information About a Microarray Experiment (MIAME) standard. We unified the data fields of GEO Data table and mapped the attributes of GEO metadata into MIAME elements. We also discriminated non-preprocessed raw datasets from others and processed ones by using a two-step classification method. Most of the procedures were developed as semi-automated algorithms with some degree of text mining techniques. We localized 2,967 Platforms, 4,867 Series and 103,590 Samples with covering 279 organisms, integrated them into a standard-based relational schema and developed a comprehensive query interface to extract. Our tool, GEOQuest is available at http://www.snubi.org/software/GEOQuest/.

• The Korean Journal of Applied Statistics
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• v.24 no.6
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• pp.1103-1113
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• 2011

Gene expression data is obtained through many stages of an experiment and errors produced during the process may cause missing values. Due to the distinctness of the data so called 'small n large p', genes have to be selected for statistical analysis, like classification analysis. For this reason, imputation and gene selection are important in a microarray data analysis. In the literature, imputation, gene selection and classification analysis have been studied respectively. However, imputation, gene selection and classification analysis are sequential processing. For this aspect, we compare the performance of classification methods after imputation and gene selection methods are applied to microarray data. Numerical simulations are carried out to evaluate the classification methods that use various combinations of the imputation and gene selection methods.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.10 no.11
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• pp.2039-2044
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• 2006

Since the bio-information now even exceeds the capability of human brain, the techniques of data mining and artificial intelligent are needed to deal with the information in this field. There are many researches about using DNA microarray technique which can obtain information from thousands of genes at once, for developing new methods of analyzing and predicting of diseases. Discovering the mechanisms of unknown genes by using these new method is expecting to develop the new drugs and new curing methods. In this Paper, We tested accuracy on classification of microarray in Bayesian method to compare normalization method's Performance after dividing data in two class that is a feature abstraction method through a normalization process which reduce or remove noise generating in microarray experiment by various factors. And We represented that it improve classification performance in 95.89% after Lowess normalization.

• Communications for Statistical Applications and Methods
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• v.25 no.5
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• pp.559-568
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• 2018

Gene classification can involve complex order-restricted inference. Examining gene expression pattern across groups with order-restriction makes standard statistical inference ineffective and thus, requires different methods. For this problem, Roy's union-intersection principle has some merit. The M-estimator adjusting for outlier arrays in a microarray study produces a robust test statistic with distribution-insensitive clustering of genes. The M-estimator in conjunction with a union-intersection principle provides a nonstandard robust procedure. By exact permutation distribution theory, a conditionally distribution-free test based on the proposed test statistic generates corresponding p-values in a small sample size setup. We apply a false discovery rate (FDR) as a multiple testing procedure to p-values in simulated data and real microarray data. FDR procedure for proposed test statistics controls the FDR at all levels of ${\alpha}$ and ${\pi}_0$ (the proportion of true null); however, the FDR procedure for test statistics based upon normal theory (ANOVA) fails to control FDR.

• Journal of the Korean Data and Information Science Society
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• v.26 no.2
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• pp.475-486
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• 2015

Mining the microarray data accumulated in the public data repositories can save experimental cost and time and provide valuable biomedical information. Big data analysis pooling multiple data sets increases statistical power, improves the reliability of the results, and reduces the specific bias of the individual study. However, integrating several data sets from different studies is needed to deal with many problems. In this study, I limited the focus to the cross platform classification that the platform of a testing sample is different from the platform of a training set, and suggested a simple classification method based on rank. This method is compared with the diagonal linear discriminant analysis, k nearest neighbor method and support vector machine using the cross platform real example data sets of two cancers.

• The KIPS Transactions:PartD
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• v.15D no.6
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• pp.767-776
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• 2008

Microarray technology is extensively being used in experimental molecular biology field. Microarray experiments generate quantitative expression measurements for thousands of genes simultaneously, which is useful for the phenotype classification of many diseases. One of the two major problems in microarray data classification is that the number of genes exceeds the number of tissue samples. The other problem is that current methods generate classifiers that are accurate but difficult to interpret. Our paper addresses these two problems. We performed a direct integration of individual microarrays with same biological objectives by transforming an expression value into a rank value within a sample and generated rank-comparison decision rules with variable number of genes for cancer classification. Our classifier is an ensemble method which has k top scoring decision rules. Each rule contains a number of genes, a relationship among involved genes, and a class label. Current classifiers which are also ensemble methods consist of k top scoring decision rules. However these classifiers fix the number of genes in each rule as a pair or a triple. In this paper we generalized the number of genes involved in each rule. The number of genes in each rule is in the range of 2 to N respectively. Generalizing the number of genes increases the robustness and the reliability of the classifier for the class prediction of an independent sample. Also our classifier is readily interpretable, accurate with small number of genes, and shed a possibility of the use in a clinical setting.

• ETRI Journal
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• v.41 no.3
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• pp.358-370
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• 2019

The main aim of this study is to select the optimal set of genes from microarray cancer datasets that contribute to the prediction of specific cancer types. This study proposes the enhancement of the feature selection filter algorithm based on Joe's normalized mutual information and its use for gene selection. The proposed algorithm is implemented and evaluated on seven benchmark microarray cancer datasets, namely, central nervous system, leukemia (binary), leukemia (3 class), leukemia (4 class), lymphoma, mixed lineage leukemia, and small round blue cell tumor, using five well-known classifiers, including the naive Bayes, radial basis function network, instance-based classifier, decision-based table, and decision tree. An average increase in the prediction accuracy of 5.1% is observed on all seven datasets averaged over all five classifiers. The average reduction in training time is 2.86 seconds. The performance of the proposed method is also compared with those of three other popular mutual information-based feature selection filters, namely, information gain, gain ratio, and symmetric uncertainty. The results are impressive when all five classifiers are used on all the datasets.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.11 no.10
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• pp.1924-1929
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• 2007

Nowadays, a lot of related data obtained from these research could be given a new present meaning to accomplish the original purpose of the whole research as a human project. The method of tumor classification based on microarray could contribute to being accurate tumor classification by finding differently expressing gene pattern statistically according to a tumor type. Therefore, the process to select a closely related informative gene with a particular tumor classification to classify tumor using present microarray technology with effect is essential. In this thesis, we used cDNA microarrays of 3840 genes obtained from neuronal differentiation experiment of cortical stem cells on white mouse with cancer, constructed accurate tumor classification model by extracting informative gene list through normalization separately and then did performance estimation by analyzing and comparing each of the experiment results. Result classifying Multi-Perceptron classifier for selected genes using Pearson correlation coefficient represented the accuracy of 95.6%.

• Journal of KIISE:Software and Applications
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• v.30 no.12
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• pp.1124-1134
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• 2003

The development of microarray technology has supplied a large volume of data to many fields. In particular, it has been applied to prediction and diagnosis of cancer, so that it expectedly helps us to exactly predict and diagnose cancer. It is essential to efficiently analyze DNA microarray data because the amount of DNA microarray data is usually very large. Since accurate classification of cancer is very important issue for treatment of cancer, it is desirable to make a decision by combining the results of various expert classifiers rather than by depending on the result of only one classifier. Generally combining classifiers gives high performance and high confidence. In spite of many advantages of ensemble classifiers, ensemble with mutually error-correlated classifiers has a limit in the performance. In this paper, we propose the ensemble of neural network classifiers learned from negatively correlated features using three benchmark datasets to precisely classify cancer, and systematically evaluate the performances of the proposed method. Experimental results show that the ensemble classifier with negatively correlated features produces the best recognition rate on the three benchmark datasets.

• Toxicological Research
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• v.22 no.4
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• pp.323-328
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• 2006

Global gene expression profile was analyzed by microarray analysis of rat liver RNA after acute acetaminophen (APAP) administration. A single dose of 1g/kg body weight of APAP was given orally, and the liver samples were obtained after 24, 48 h, and 2 weeks. Histopathologic and biochemical studies enabled the classification of the APAP effect into injury (24 and 48 h) and regeneration (2 weeks) stages. The expression levels of 4900 clones on a custom rat gene microarray were analyzed and 484 clones were differentially expressed with more than a 1.625-fold difference(which equals 0.7 in log2 scale) at one or more time points. Two hundred ninety seven clones were classified as injury-specific clones, while 149 clones as regeneration-specific ones. Characteristic gene expression profiles could be associated with APAP-induced gene expression changes in lipid metabolism, stress response, and protein metabolism. We established a global gene expression profile utilizing microarray analysis in rat liver upon acute APAP administration with a full chronological profile that not only covers injury stage but also later point of regeneration stage.