In this relatively new technology, DNA fragments representing known sequences of genes are synthesized on silicon chips using technology related to that used to produce computer chips. Samples of RNA (the expressed genes) - in this case, RNA from the rat kidney - are labeled with fluorescent dye and applied to the gene chip. The RNA binds to just the DNA fragments on the chip with the correct, or complimentary sequence, thus indicating which rat kidney genes are activated at specific points in time. As the precise position of the highlighted DNA fragments on the chip is known, a computer can deconstruct a chip image into thousands of numbers.
However, the challenge has been the interpretation of the complex data provided by the chips. The field is relatively young and the few commercial software applications designed for gene expression analysis don't meet all needs. Stuart wrote customized programs - called Equalizer and eBlot to track gene expression and organize the findings into meaningful groups. The goal was to separate activated genes from the unchanging "housekeeping" genes.
"The thousands of housekeeping genes represent the haystack in which the needles - or genes that turn on or off during development - are buried," Stuart says. "Our goal was to whittle away all the chaff in the haystack by placing each gene expression measurement in the context of all the others."
First, the investigators isolated RNA from embryonic rats at gestational days 13, 15, 17 and 19, at birth, one week of age, and as non-pregnant adults. The researchers used DNA chips and their custom tools to identify 873 kidney genes out of 8,740 genes present on the DNA chips that significantly changed expression during development. These genes clustered into five distinct groups, based on their peak expression during development:
The first stage of development focused on prol
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Contact: Sue Pondrom
spondrom@ucsd.edu
619-543-6163
University of California - San Diego
30-Apr-2001