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We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data

Cluster Analysis And Display Of Genome-Wide Expression Patterns

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, no. 25 (1998): 14863-14868

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摘要

A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a f...更多

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简介
  • Sources of Experimental Data.
  • Gene expression of primary human fibroblasts stimulated with serum following serum starvation was studied by using a microarray with 9,800 cDNAs representing approximately 8,600 distinct human transcripts [11].
  • RNA from experimental samples was labeled during reverse transcription with the red-fluorescent dye Cy5 (Amersham) and was mixed with a reference sample labeled in parallel with the green-fluorescent dye Cy3 (Amersham).
  • After hybridization and appropriate washing steps, separate images were acquired for each fluor, and fluorescence intensity ratios were obtained for all target element
重点内容
  • A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression
  • We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data
  • Gene expression in the budding yeast Saccharomyces cerevisiae was studied during the diauxic shift [8], the mitotic cell division cycle [9], sporulation [10], and temperature and reducing shocks (P.T.S., P.O.B., and D.B., unpublished results) by using microarrays containing essentially every ORF from this fully sequenced organism [8]
  • No similar structure resulted from any of these randomized data sets, indicating that the patterns seen in Figs. 1 and 2 depict biological order in the gene expression response of the organism during the studied processes
方法
  • Sources of Experimental Data.
  • Gene expression of primary human fibroblasts stimulated with serum following serum starvation was studied by using a microarray with 9,800 cDNAs representing approximately 8,600 distinct human transcripts [11].
  • RNA from experimental samples was labeled during reverse transcription with the red-fluorescent dye Cy5 (Amersham) and was mixed with a reference sample labeled in parallel with the green-fluorescent dye Cy3 (Amersham).
  • After hybridization and appropriate washing steps, separate images were acquired for each fluor, and fluorescence intensity ratios were obtained for all target elements
结果
  • The authors applied this method to two sets of data, a single time course (Fig. 1) of a canonical model of the growth response in human cells [11] and an aggregation of data from experiments on the budding yeast S. cerevisiae (Fig. 2), including time courses of the mitotic cell division cycle [9], sporulation [10], the diauxic shift [8], and shock responses (P.T.S., P.O.B., and D.B., unpublished results).
  • 1 and 2 is the presence of large contiguous patches of color representing groups of genes that share similar expression patterns over multiple conditions.
  • To verify that this structure is of biological origin and is not an artifact of the clustering procedure, the initial data from the human growth response experiment were randomized in three different ways and were clustered by using the same procedure (Fig. 3).
  • An important test of the value of this approach comes when the authors examine the identity of the clustered genes at varying levels of identity
结论
  • Microarray-based genomic surveys and other high-throughput approaches are becoming increasingly important in biology and chemistry.
  • Recognizing that the rate-limiting step in exploring and searching large tables of numerical data is a trivial one: reading the numbers, the authors represent the quantitative values in the table by using a naturalistic color scale rather than numbers
  • This alternative encoding preserves all the quantitative information, but transmits it to the brains by way of a much higher-bandwidth channel than the ‘‘number-reading’’ channel
表格
  • Table1: Identification of the most abundant signals in the ESI mass spectra of total lipid extract of CHO cells, as given in Fig. 1 a and b
Download tables as Excel
基金
  • This work was supported by a grants from the National Institutes of Health (GM 46406, HG 00983, and CA77097)
  • P.T.S. was supported by a training grant from the National Eye Institute (Bethesda, MD)
  • M.B.E. was supported by a postdoctoral fellowship from the Alfred E
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