developmental stage/trend analysis for gene expression

Jonathan Epstein Jonathan_Epstein at nih.gov
Tue Jul 30 15:30:07 EST 2002


Hi,

Are there techniques which evaluate the up- and down- regulation of genes
across a series of different developmental stages?

E.g., suppose that one had microarray or SAGE data collected over 5
different developmental stages, e.g. (for zebrafish, which I know best) (a)
bud, (b) shield, (c) 10 somite, (d) 15 somite, (e) 20 somite.

Suppose that genes A and B are up-regulated in the bud stage in microArray's
X, Y and Z. Similarly A and B are up-regulated in all of the other
developmental stages using the same microArray's.

Conversely suppose that genes C and D are both down-regulated in bud stage
and 10 somite, but both are up-regulated in shield stage and 15 somite,
while in 20-somite stage C is up-regulated and D shows no significant up- or
down- regulation.

What software packages and computational techniques are typically used to
handle this sort of trend analysis? The matching of the trends doesn't look
that complicated, but I'm sure that there are well established techniques
for dealing with this data, especially when there are less black-and-white
scenarios that what I've described above.

We have found the following, which looks very promising, but wonder what
else might be out there, especially open source solutions.

http://www.genomethods.org/caged/about.htm

Thanks in advance,

- Jonathan








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