Cluster analysis of gene expression data
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Abstract: The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical experiment uses a few tens of such chips, each dedicated to a single sample - such as tissue extracted from a particular tumor. The results of such an experiment contain several hundred thousand numbers, that come in the form of a table, of several thousand rows (one for each gene) and 50 - 100 columns (one for each sample). We developed a clustering methodology to mine such data. In this review I provide a very basic introduction to the subject, aimed at a physics audience with no prior knowledge of either gene expression or clustering methods. I explain what genes are, what is gene expression and how it is measured by DNA chips. Next I explain what is meant by "clustering" and how we analyze the massive amounts of data from such experiments, and present results obtained from analysis of data obtained from colon cancer, brain tumors and breast cancer.
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- scientific article; zbMATH DE number 5274665 (Why is no real title available?)
- Mooshka: A system for the management of multidimensional gene expression data in situ.
- A Method of Finding Predictor Genes for a Particular Disease Using a Clustering Algorithm
- Predicting Gene Function using Predictive Clustering Trees
- Clustering Dependencies with Support Vectors
- Graph clustering and visualizing methods on genomic data
- scientific article; zbMATH DE number 5260683 (Why is no real title available?)
- Simulated annealing based automatic fuzzy clustering combined with ANN classification for analyzing microarray data
- Clustering gene expression data using a posterior split-merge-birth procedure
- Towards improving fuzzy clustering using support vector machine: application to gene expression data
- Extracting information from cDNA arrays
- Determining distinct clusters in gene expression data using similarity in principal component subspaces
- Advances in Neural Networks – ISNN 2005
- Clustering of microarray data via clique partitioning
- A Generalized Clustering Problem, with Application to DNA Microarrays
- Problems in gene clustering based on gene expression data
- A new approach: interrelated two-way clustering of gene expression data
- The Clustering of Regression Models Method with Applications in Gene Expression Data
- GeneMCL in microarray analysis
- Topological analysis of gene expression arrays identifies high risk molecular subtypes in breast cancer
- scientific article; zbMATH DE number 1750181 (Why is no real title available?)
- scientific article; zbMATH DE number 2148860 (Why is no real title available?)
- Clapper: a clustering algorithm based on path-distances for experimental replicates
- Clustering Short Gene Expression Profiles
- Tumor classification using phylogenetic methods on expression data
- State-of-the-art of Cluster Analysis of Gene Expression Data
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