• Molecules and Cells
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• v.25 no.2
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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.

• Journal of the Institute of Electronics Engineers of Korea CI
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• v.42 no.1
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• pp.1-7
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• 2005

Cluster analysis of microarray data has been often used to find biologically relevant Broups of genes based on their expression levels. Since many functionally related genes tend to be co-expressed, by identifying groups of genes with similar expression profiles, the functionalities of unknown genes can be inferred from those of known genes in the same group. In this Paper we address a novel clustering approach, called seed clustering, and investigate its applicability for microarray data analysis. In the seed clustering method, seed genes are first extracted by computational analysis of their expression profiles and then clusters are generated by taking the seed genes as prototype vectors for target clusters. Since it has strong mathematical foundations, the seed clustering method produces the stable and consistent results in a systematic way. Also, our empirical results indicate that the automatically extracted seed genes are well representative of potential clusters hidden in the data, and that its performance is favorable compared to current approaches.

• Animal cells and systems
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• v.9 no.1
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• pp.1-7
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• 2005

Class I and class II MHC genes have been identified in most of the jawed vertebrate taxa. In all investigated bony fish species, unlike mammals, the classical class I and class II MHC genes are not linked and even are found on different chromosomes. Linking and clustering of the class I and class II MHC genes is not the only phenomenon clearly detected in the evolution of immune system from cartilaginous to mammals. In all non-mammalian classes the LMP/TAP genes are highly conserved within class I genes region, while these genes are conserved within class II genes region only in mammals. Today we know that LMP/TAP genes in mammals have a crucial role in peptide processing for presentation within class I molecules, as well as in anti-tumor immunity. For these reasons, differences in clustering of LMP/TAP/MHC genes can be responsible for the differences in mechanisms and efficacy of anti-tumor immunity in non-mammalian vertebrates compared to same mechanisms in mammals. Also, the differences in cytokine network and anti-tumor antigens presentation within classes of vertebrates can be explained by toe peculiarity of LMP/TAP/MHC gene clustering.

• Genomics & Informatics
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• v.9 no.2
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• pp.89-91
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• 2011

DNA chips are becoming increasingly popular as a convenient way to perform vast amounts of experiments related to genes on a single chip. And the importance of analyzing the data that is provided by such DNA chips is becoming significant. A very important analysis on DNA chip data would be clustering genes to identify gene groups which have similar properties such as cancer. Clustering data for DNA chips usually deal with a large search space and has a very fuzzy characteristic. The Particle Swarm Optimization algorithm which was recently proposed is a very good candidate to solve such problems. In this paper, we propose a clustering mechanism that is based on the Particle Swarm Optimization algorithm. Our experiments show that the PSO-based clustering algorithm developed is efficient in terms of execution time for clustering DNA chip data, and thus be used to extract valuable information such as cancer related genes from DNA chip data with high cluster accuracy and in a timely manner.

• Communications for Statistical Applications and Methods
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• v.13 no.1
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• pp.113-123
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• 2006

Normal mixture model(NMM) frequently used to cluster genes on microarray gene expression data. In this paper some of component means of NMM are modelled by a linear regression model so that its design matrix presents the pattern between sample classes in microarray matrix. This modelling for the component means by given design matrices certainly has an advantage that we can lead the clusters that are previously designed. However, it suffers from 'overfitting' problem because in practice genes often are highly dimensional. This problem also arises when the NMM restricted by the linear model for component-means is fitted. To cope with this problem, in this paper, the use of the factor analyzer NMM restricted by linear model is proposed to cluster genes. Also several design matrices which are useful for clustering genes are provided.

• Genomics & Informatics
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• v.5 no.1
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• pp.10-18
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• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• Communications for Statistical Applications and Methods
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• v.12 no.2
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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.

• International Journal of Contents
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• v.8 no.1
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• pp.23-29
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• 2012

Multiple expression levels of genes obtained using time series microarray experiments have been exploited effectively to enhance understanding of a wide range of biological phenomena. However, the unique nature of microarray data is usually in the form of large matrices of expression genes with high dimensions. Among the huge number of genes presented in microarrays, only a small number of genes are expected to be effective for performing a certain task. Hence, discounting the majority of unaffected genes is the crucial goal of gene selection to improve accuracy for disease diagnosis. In this paper, a non-Gaussian weight matrix obtained from an incremental model is proposed to extract useful features of multivariate time series microarrays. The proposed method can automatically identify a small number of significant features via discovering hidden variables from a huge number of features. An unsupervised hierarchical clustering representative is then taken to evaluate the effectiveness of the proposed methodology. The proposed method achieves promising results based on predictive accuracy of clustering compared to existing methods of analysis. Furthermore, the proposed method offers a robust approach with low memory and computation costs.

• Communications for Statistical Applications and Methods
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• v.14 no.3
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• pp.687-698
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• 2007

A normal mixture model with which dependence between classes is incorporated is proposed in order to detect differentially expressed genes. Gene clustering approaches suffer from the high dimensional column of microarray expression data matrix which leads to the over-fit problem. Various methods are proposed to solve the problem. In this paper, use of simple averaging data within each class is proposed to overcome the various problems due to high dimensionality when the normal mixture model is fitted. Some experiments through simulated data set and real data set show its availability in actuality.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.748-756
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• 2006

We propose a genome-scale clustering approach to identify whole genome relationships using the functional groups given by the Kyoto Encyclopedia of Genes and Genomes Orthology (KO) database. The metabolic capabilities of each organism were defined by the number of genes in each functional category. The archaeal, bacterial, and eukaryotic genomes were compared by simultaneously applying a two-step clustering method, comprised of a self-organizing tree algorithm followed by unsupervised hierarchical clustering. The clustering results were consistent with various phenotypic characteristics of the organisms analyzed and, additionally, showed a different aspect of the relationship between genomes that have previously been established through rRNA-based comparisons. The proposed approach to collect and cluster the metabolic functional capabilities of organisms should make it a useful tool in predicting relationships among organisms.