• The Korean Journal of Applied Statistics
• /
• v.19 no.1
• /
• pp.13-32
• /
• 2006

Biologists are attempting to group genes based on the temporal pattern of gene expression levels. So far, a number of methods have been proposed for clustering microarray data. However, the results of clustering depends on the genes selection, therefore the gene selection with significant expression difference is also very important to cluster for microarray data. Thus, this paper present the results of broad comparative studies to time course microarray data by considering methods of gene selection, clustering and cluster validation.

• The Korean Journal of Applied Statistics
• /
• v.24 no.4
• /
• pp.623-631
• /
• 2011

A major goal of time-course microarray data analysis is the detection of groups of genes that manifest similar expression patterns over time. The corresponding numerous cluster algorithms for clustering time-course microarray data have been developed. In this study, we proposed a clustering method based on the primary pharmacokinetic parameters in the pharmacokinetics study for assessment of pharmaceutical equivalents between two drug products. A real data and a simulation data was used to demonstrate the usefulness of the proposed method.

• The Korean Journal of Applied Statistics
• /
• v.18 no.2
• /
• pp.371-379
• /
• 2005

In this paper, we propose a pattern consistency index for detecting heterogeneous time series that deviate from the representative pattern of each cluster in clustering time course gene expression data using the Pearson correlation coefficient. We examine its usefulness by applying this index to serum time course gene expression data from microarrays.

• The Korean Journal of Applied Statistics
• /
• v.33 no.3
• /
• pp.269-280
• /
• 2020

Time course gene expression data is a large amount of data observed over time in microarray experiments. This data can also simultaneously identify the level of gene expression. However, the experiment process is complex, resulting in frequent missing values due to various causes. In this paper, we propose a pattern consistency index adaptive nearest neighbors as a method of missing value imputation. This method combines the adaptive nearest neighbors (ANN) method that reflects local characteristics and the pattern consistency index that considers consistent degree for gene expression between observations over time points. We conducted a Monte Carlo simulation study to evaluate the usefulness of proposed the pattern consistency index adaptive nearest neighbors (PANN) method for two yeast time course data.

• The Korean Journal of Applied Statistics
• /
• v.23 no.4
• /
• pp.705-713
• /
• 2010

Predicting survival from microarray data is not easy due to the problem of high dimensionality of data and the existence of censored observations. Also the limitation of individual gene analysis causes the shift of focus to the level of gene sets with functionally related genes. For developing a survival prediction model based on pathway information, the methods for selecting a supergene using principal component analysis and testing its significance for each pathway are discussed. Besides, the performance of gene filtering is compared.

• The Korean Journal of Applied Statistics
• /
• v.21 no.2
• /
• pp.275-290
• /
• 2008

The size of microarray gene expression data is very big and its observation process is also very complex. Thus missing values are frequently occurred. In this paper we propose the sequential partial least squares(SPLS) regression fitting method to estimate missing values for time course gene expression data that has correlations among observations over time points. The SPLS method is to combine the sequential technique with the partial least squares(PLS) regression fitting method. The usefulness of method proposed is evaluated through some simulation study for three yeast time course data.

• Journal of the Korean Data and Information Science Society
• /
• v.23 no.1
• /
• pp.1-11
• /
• 2012

When the microarray experiment developed, main interest was limited to detect differentially expressed genes associated with a phenotype of interest. However, as human diseases are thought to occur through the interactions of multiple genes within a same functional category, the unit of analysis of the microarray experiment expanded to the set of genes. For the phenotype of censored survival time, Gene Set Enrichment Analysis(GSEA), Global test and Wald type test are widely used. In this paper, we modified the Wald type test by adopting normal score transformation of gene expression values and developed a parametric test which requires much less computation than others. The proposed method is compared with other methods using a real data set of ovarian cancer and a simulation data set.

• Journal of the Korean Data and Information Science Society
• /
• v.25 no.5
• /
• pp.1079-1094
• /
• 2014

In this paper, we study efficient gene selection methods by using conditional mutual information. We suggest gene selection methods using conditional mutual information based on semiparametric methods utilizing multivariate normal distribution and Edgeworth approximation. We compare our suggested methods with other methods such as mutual information filter, SVM-RFE, Cai et al. (2009)'s gene selection (MIGS-original) in SVM classification. By these experiments, we show that gene selection methods using conditional mutual information based on semiparametric methods have better performance than mutual information filter. Furthermore, we show that they take far less computing time than Cai et al. (2009)'s gene selection but have similar performance.