Binary tree-structured vector quantization approach to clustering and visualizing microarray data

Motivation: With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data a...

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Vydané v:Bioinformatics Ročník 18; číslo suppl_1; s. S111 - S119
Hlavní autori: Sultan, M., Wigle, D.A., Cumbaa, C.A., Maziarz, M., Glasgow, J., Tsao, M.S., Jurisica, I.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Oxford Publishing Limited (England) 01.07.2002
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Abstract Motivation: With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into ‘meaningful’ groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified. Results: Starting with a systematic comparison of the underlying theories behind clustering approaches, we have devised a technique that combines tree-structured vector quantization and partitive k-means clustering (BTSVQ). This hybrid technique has revealed clinically relevant clusters in three large publicly available data sets. In contrast to existing systems, our approach is less sensitive to data preprocessing and data normalization. In addition, the clustering results produced by the technique have strong similarities to those of self-organizing maps (SOMs). We discuss the advantages and the mathematical reasoning behind our approach. Availability: The BTSVQ system is implemented in Matlab R12 using the SOM toolbox for the visualization and preprocessing of the data http://www.cis.hut.fi/projects/somtoolbox/ BTSVQ is available for non-commercial use http://www.uhnres.utoronto.ca/ta3/BTSVQ Contact: ij@uhnres.utoronto.ca Keywords: microarray data clustering and visulization; self-organizing maps, partitive k-means clustering; lung cancer.
AbstractList Motivation: With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into 'meaningful' groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified. Results: Starting with a systematic comparison of the underlying theories behind clustering approaches, we have devised a technique that combines tree-structured vector quantization and partitive k-means clustering (BTSVQ). This hybrid technique has revealed clinically relevant clusters in three large publicly available data sets. In contrast to existing systems, our approach is less sensitive to data preprocessing and data normalization. In addition, the clustering results produced by the technique have strong similarities to those of self-organizing maps (SOMs). We discuss the advantages and the mathematical reasoning behind our approach. Availability: The BTSVQ system is implemented in Matlab R12 using the SOM toolbox for the visualization and preprocessing of the data http://www.cis.hut.fi/projects/somtoolbox/ BTSVQ is available for non-commercial use http://www.uhnres.utoronto.ca/ta3/BTSVQ Contact: ij[at]uhnres.utoronto.ca Keywords: microarray data clustering and visulization; self-organizing maps, partitive k-means clustering; lung cancer.
Motivation: With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into ‘meaningful’ groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified. Results: Starting with a systematic comparison of the underlying theories behind clustering approaches, we have devised a technique that combines tree-structured vector quantization and partitive k-means clustering (BTSVQ). This hybrid technique has revealed clinically relevant clusters in three large publicly available data sets. In contrast to existing systems, our approach is less sensitive to data preprocessing and data normalization. In addition, the clustering results produced by the technique have strong similarities to those of self-organizing maps (SOMs). We discuss the advantages and the mathematical reasoning behind our approach. Availability: The BTSVQ system is implemented in Matlab R12 using the SOM toolbox for the visualization and preprocessing of the data http://www.cis.hut.fi/projects/somtoolbox/ BTSVQ is available for non-commercial use http://www.uhnres.utoronto.ca/ta3/BTSVQ Contact: ij@uhnres.utoronto.ca Keywords: microarray data clustering and visulization; self-organizing maps, partitive k-means clustering; lung cancer.
Motivation: With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into 'meaningful' groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified. Results: Starting with a systematic comparison of the underlying theories behind clustering approaches, we have devised a technique that combines tree-structured vector quantization and partitive k-means clustering (BTSVQ). This hybrid technique has revealed clinically relevant clusters in three large publicly available data sets. In contrast to existing systems, our approach is less sensitive to data preprocessing and data normalization. In addition, the clustering results produced by the technique have strong similarities to those of self-organizing maps (SOMs). We discuss the advantages and the mathematical reasoning behind our approach. Availability: The BTSVQ system is implemented in Matlab R12 using the SOM toolbox for the visualization and preprocessing of the data http://www.cis.hut.fi/projects/somtoolbox/ BTSVQ is available for non-commercial use http://www.uhnres.utoronto.ca/ta3/BTSVQ Contact: ij@uhnres.utoronto.ca Keywords: microarray data clustering and visulization; self-organizing maps, partitive k-means clustering; lung cancer.
With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into 'meaningful' groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified.MOTIVATIONWith the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into 'meaningful' groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified.Starting with a systematic comparison of the underlying theories behind clustering approaches, we have devised a technique that combines tree-structured vector quantization and partitive k-means clustering (BTSVQ). This hybrid technique has revealed clinically relevant clusters in three large publicly available data sets. In contrast to existing systems, our approach is less sensitive to data preprocessing and data normalization. In addition, the clustering results produced by the technique have strong similarities to those of self-organizing maps (SOMs). We discuss the advantages and the mathematical reasoning behind our approach.RESULTSStarting with a systematic comparison of the underlying theories behind clustering approaches, we have devised a technique that combines tree-structured vector quantization and partitive k-means clustering (BTSVQ). This hybrid technique has revealed clinically relevant clusters in three large publicly available data sets. In contrast to existing systems, our approach is less sensitive to data preprocessing and data normalization. In addition, the clustering results produced by the technique have strong similarities to those of self-organizing maps (SOMs). We discuss the advantages and the mathematical reasoning behind our approach.
With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into 'meaningful' groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified. Starting with a systematic comparison of the underlying theories behind clustering approaches, we have devised a technique that combines tree-structured vector quantization and partitive k-means clustering (BTSVQ). This hybrid technique has revealed clinically relevant clusters in three large publicly available data sets. In contrast to existing systems, our approach is less sensitive to data preprocessing and data normalization. In addition, the clustering results produced by the technique have strong similarities to those of self-organizing maps (SOMs). We discuss the advantages and the mathematical reasoning behind our approach.
With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have successfully been applied to unravel latent similarities among genes and/or experiments. Most of the current systems for microarray data analysis use statistical methods, hierarchical clustering, self-organizing maps, support vector machines, or k-means clustering to organize genes or experiments into 'meaningful' groups. Without prior explicit bias almost all of these clustering methods applied to gene expression data not only produce different results, but may also produce clusters with little or no biological relevance. Of these methods, agglomerative hierarchical clustering has been the most widely applied, although many limitations have been identified.
Author Cumbaa, C.A.
Wigle, D.A.
Tsao, M.S.
Jurisica, I.
Glasgow, J.
Sultan, M.
Maziarz, M.
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/12169538$$D View this record in MEDLINE/PubMed
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Snippet Motivation: With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques...
With the increasing number of gene expression databases, the need for more powerful analysis and visualization tools is growing. Many techniques have...
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SubjectTerms Algorithms
Carcinoma, Non-Small-Cell Lung - genetics
Cluster Analysis
Computer Graphics
Gene Expression Profiling - methods
Humans
Lung cancer
Lung Neoplasms - genetics
Models, Genetic
Models, Statistical
Oligonucleotide Array Sequence Analysis - methods
Software
Statistical methods
User-Computer Interface
Title Binary tree-structured vector quantization approach to clustering and visualizing microarray data
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