Program of the 2001 International Worm Meeting - Sternberg Lab ...

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10. A gene expression map for C.
elegans
Stuart K. Kim 1 , Jim Lund 1 , Stewart
Scherer 2 , Moni Kiraly 1 , Kyle Duke 1 ,
Min Jiang 1 , Brian N. Wylie 3 , George
S. Davidson 3
1 Department of Developmental Biology and
GeneticsStanford University Medical
SchoolStanford CA 94305
2 3938 Paseo GrandeMoraga, CA 94556
3 Computation, Computers and Mathematics
CenterSandia National
LaboratoriesAlbuquerque, New Mexico
87185-0318
The completion of the C. elegans genome
sequence has identified nearly all of the genes in
the genome (19,282 genes), but the function for
most of these genes remains mysterious. A scant
6% of them have been studied using classical
genetic or biochemical approaches (1135
genes), and only about 53% show homology to
genes in other organisms (10,303 genes). The
next challenge is to develop high-throughput,
functional genomics procedures to study many
genes in parallel in order to elucidate gene
function on a global scale. One such approach is
to use DNA microarrays to assay the relative
expression of nearly every gene in the genome
between two samples. Knowing when, where
and under which conditions a particular gene is
expressed can reveal the function of that gene.
A consortium of laboratories has used C.
elegans DNA microarrays to profile gene
expression changes in a wide variety of
experiments. In each experiment, RNA from
one sample was used to generate Cy3-labelled
cDNA, and RNA from another sample was used
to prepare Cy5-labelled cDNA. The two cDNA
probes were simultaneously hybridized to a
single DNA microarray and the ratio of the Cy3
to Cy5 hybridization intensities was measured,
revealing which genes were relatively enriched
in either RNA sample. Thirty different
laboratories have collectively performed 553
experiments using these C. elegans DNA
microarrays, including 179 experiments with
microarrays containing 11,917 genes (63% of
the genome) and 370 experiments using
microarrays that have 17,817 genes (94% of the
genome). The experiments compare RNA
between mutant and wild-type strains, or
between worms grown under different
conditions. Many experiments have been done
to date, including experiments on wild-type
development, heat shock, Ras signaling, aging,
the dauer stage, sex regulation and germ line
gene expression. Individual microarray
experiments reveal sets of genes that change in
one mutant strain or growth condition. We
combine the data from all of the experiments to
assemble a gene expression database, and then
used this database to group together
co-regulated genes and visualize them using a
three dimensional expression map. By matching
the expression profile of an unknown gene to
those of genes with known functions, the
expression map can be used to ascribe functions
to the large fraction of genes in the genome
whose functions were previously unknown.
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