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 -- ================================================================== 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/ ==================================================================