Dear all,
The first run of ENIGMA on the cell cycle data has been completed. Out
of 500+ experiments, approx 300 qualified as perturbational and could
be used directly by ENIGMA. 120 of those featured less than 10
differentially expressed genes. These were discarded, the other 180
were kept. You can view the results in the folder
stmae/enigma_cell_cycle on the psb drive (P:). For interpretation of
the result files, see the ENIGMA website (http://bioinformatics.psb.ugent.be/ENIGMA/main.htm),
for interpretation of the figures, see the legend of the sample figure
below. Bear in mind that this is the first run, there are some things
that I plan to check/improve, such as (i) discard experiments with
pleiotropic effects, these tend to give rise to unnaturally large
modules that may mask smaller modules (see e.g. first module figures)
(ii) try to include more data that was not yet included in the
compendium and/or did not qualify directly for use by ENIGMA (iii)
reconsider the preprocessing protocol, include more informative
experiment labels, update Arabidopsis GO data and include Arabidopsis
TF motif data if possible. I'm gone on holidays until thursday August
16th, I'm interested in any suggestions/comments you might have by
then.
Best,
Steven
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Steven Maere, PhD
Dept. of Plant Systems Biology
Bioinformatics & Evolutionary Genomics research group
VIB / Ghent University
Technologiepark 927
B-9052 Gent BELGIUM
tel: +32 9 331 3810
fax: +32 9 331 3809
email: stmae@psb.UGent.be
http://www.psb.UGent.be
http://bioinformatics.psb.ugent.be/
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