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Science 27 October 2000:
Vol. 290. no. 5492, pp. 809 - 812
DOI: 10.1126/science.290.5492.809

Reports

Genomic Analysis of Gene Expression in C. elegans

A. A. Hill,1* C. P. Hunter,2* B. T. Tsung,2 G. Tucker-Kellogg,1 †E. L. Brown1

Until now, genome-wide transcriptional profiling has been limited to single-cell organisms. The nematode Caenorhabditis elegans is a well-characterized metazoan in which the expression of all genes can be monitored by oligonucleotide arrays. We used such arrays to quantitate the expression of C. elegans genes throughout the development of this organism. The results provide an estimate of the number of expressed genes in the nematode, reveal relations between gene function and gene expression that can guide analysis of uncharacterized worm genes, and demonstrate a shift in expression from evolutionarily conserved genes to worm-specific genes over the course of development.

1 Department of Genomics, Genetics Institute, Cambridge, MA 02140, USA.
2 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
*   To whom correspondence should be addressed. E-mail: ahill{at}genetics.com (A.A.H.) and hunter{at}mcb.harvard.edu (C.P.H.)


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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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