Broad patterns of gene expression revealed by clustering analysis of tumorand normal colon tissues probed by oligonucleotide arrays

Oligonucleotide arrays can provide a broad picture of the state of the cell , by monitoring the expression level of thousands of genes at the same time . It is of interest to develop techniques for extracting useful information from the resulting data sets. Here we report the application of a two-way clustering method for analyzing a data set consisting of the expression pat terns of different cell types. Gene expression in 40 tumor and 22 normal co lon tissue samples was analyzed with an Affymetrix oligonucleotide array co mplementary to more than 6,500 human genes. An efficient two way clustering algorithm was applied to both the genes and the tissues, revealing broad c oherent patterns that suggest a high degree of organization underlying gene expression in these tissues. Coregulated families of genes clustered toget her, as demonstrated for the ribosomal proteins. Clustering also separated cancerous from noncancerous tissue and cell lines from in vivo tissues on t he basis of subtle distributed patterns of genes even when expression of in dividual genes varied only slightly between the tissues, Two-way clustering thus may be of use both in classifying genes into functional groups and in classifying tissues based on gene expression.