AFGC Microarray Database

Katrina Katrina at Andrew2.stanford.edu
Thu Aug 12 20:41:19 EST 1999


The Arabidopsis Functional Genomics Group (AFGC) is currently developing
an Oracle database that will house the microarray data from the several
hundred  Arabidopsis experiments that will be performed sometime next
year.

When the time comes to analyze this data, it will be critical to know
the experimental conditions each researcher used prior to RNA
extraction.  Since this data will eventually be public, everyone will
get a chance to cluster groups of experiments and to perform there own
analysis.  We'd like to get a clear sense of what you'd like to search
for, and which parameters are the most critical.  Once we know what the
community requires, we can design the database to be as useful as
possible so everyone can benefit..

Once selected by NSF, each experimenter will be asked to fill out a web
based form giving the critical elements of his/her work, as well as some
keywords that fit the project and probably a more detailed abstract.  So
while we'd all like know know as much as possible it's unlikely that
each and every experimenter want to provide soil moisture content in
standard units or leaf area index.  Only when those variables are
critical to the a given experiment will they be expected.

Some of the critical elements are very clear, such as genotype.  Was the
RNA extracted from a wild type plant, a mutant or a transgenic?  What is
the ecotype of the plant? (i.e. Colomibia , Landsberg, ws, c24, etc.),
is the Accession known? is there an ABRC ID#?  This kind of information
will likely be required.  We'll also like to know which ecotypes are
likely to used and how exhaustive the pop-up lists we're envisioning
need to be.

There are of course a many other questions concerning growth conditions,
growing media, light quality.  For now though I'd  just like to hear
from any interested parties about a few simple questions.

What are the number and types of ecotypes people like to use?

Would you only examine microarray data from a single ecotype or are you
likely to look more broadly?

Concerning mutant lineages are you more likely to be interested in a
mutant because of  the pathway or process it targets or would you be
interested in clustering T-DNA mutants versus EMS mutants?

David Finkelstein
(post-doc in bioinformatics)
Carnegie Institute of Washington
Dept. of Plant Biology
260 Panama Street
Stanford, CA
e-mail:
finkel at genome.stanford.edu






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