August 2007 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] cell cycle data subsets
by Steven Maere 17 Aug '07

17 Aug '07

Hi, I've divided the cell cycle data in 4 subsets (cc_subset_x in test_data folder) based on complete linkage hierarchical clustering (using Pearson's correlation as similarity measure). There's cell cycle genes in all 4 sets, but subset_3 has most of them (42/87, see .bgo files). Please be aware that when running LeMoNe and successors on these subsets, you make the assumption that not many genes of different subsets ought to end up in the same module. Another preprocessing step that I would like you to consider is to mean-normalize the genewise expression profiles (mean 0, unit stdev) before running LeMoNe, so that genes with similar behavior but different amplitude would end up in the same module. Currently, the expression profiles are not mean-normalized, it's better to provide this option in the program... Cheers, 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(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] we should briefly discuss this one of the next days ... a lot concerns you guys and girls! Yves
by Yves Van de Peer 13 Aug '07

13 Aug '07

-------- Original Message -------- Subject: Agenda brainstorm Date: Mon, 13 Aug 2007 15:50:09 +0200 From: Dirk Inze <dirk.inze(a)psb.UGent.be> To: <mc(a)psb.UGent.be> CC: Hilde Diegenant <hidie(a)psb.UGent.be> Dear All, please find a new version of the agenda with incoorperated comments of Gerrit and Wout. I hope to finalize it by wednesday. With kind regards Dirk -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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Re: [Beg-sysbiol] systems biology
by Yves Van de Peer 12 Aug '07

12 Aug '07

Yvan Saeys wrote: > Hi Yves, > > As far as Sofie and me concerns, the following two topics are related > to systems biology: > > -text mining approaches to extract knowledge from literature, and thus > enhance/complement/improve other sysbiol approaches > -integration of heterogeneous data sources, both from a data basing > (see thesis Sofie) and a data mining approach (which are the best > techniques for combining data, how can we get more info by combining > things, how can we design new data mining and machine learning > techniques to reason with these different sources of data). > > What do we already have available: the GeneFetch system developed > during the thesis of Sofie, and hopefully a Bioinformatics article in > the following months. The database underlying GeneFetch can already > be used by other people/programs too, but still has to be extended to > other organisms (but this will be quite easy). Later on, we hope to > get some biological validation/feedback, first from the people from > SCK-CEN in Mol when they will start using the tool (probably beginnin > of september, Sofie is giving an initation there at the end of August). Perfect! Tom, steek jij dit in een documentje? Alvast bedankt. Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] systems biology
by Yves Van de Peer 12 Aug '07

12 Aug '07

Dear All, Soon, August 23 and 24, all PIs have a brainstorm meeting to discuss the future and further strategy of the PSB department. Systems Biology approaches will be high on the agenda, and I was elected :-) to lead the discussion on Systems Biology in the Department. Therefore, I'm trying to compile a list or number of topics that we are already working on and that could be considered systems biology. The idea is to show that we are already doing quite a bit in this field, because it is a general complaint from the experimental labs that nothing (or very little) happens in the department (in a way, many expect some magic analyses to come the computational groups :-). I would like to counter this as much as possible. Therefore, if you all could send me, in a few lines, what topics/subjects your working on and that you consider systems biology projects, please have them compiled (Tom, can you do that?) and send them to me. Many thanks in advance, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] A Predicted Interactome for Arabidopsis. [Plant Physiol. 2007] - PubMed Result
by Yves Van de Peer 12 Aug '07

12 Aug '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=…

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[Beg-sysbiol] MOVE: A Multi-level Ontology-based Visualization a...[In Silico Biol. 2007] - PubMed Result
by Yves Van de Peer 12 Aug '07

12 Aug '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=…

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[Beg-sysbiol] Innovation and robustness in complex regulatory ge...[Proc Natl Acad Sci U S A. 2007] - PubMed Result
by Yves Van de Peer 12 Aug '07

12 Aug '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=…

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[Beg-sysbiol] enigma on cell cycle data (with figure)
by Steven Maere 08 Aug '07

08 Aug '07

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[Beg-sysbiol] enigma on cell cycle data
by Steven Maere 08 Aug '07

08 Aug '07

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(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] Increased glycolytic flux as an outcome of whole-g...[Mol Syst Biol. 2007] - PubMed Result
by Yves Van de Peer 05 Aug '07

05 Aug '07

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=…

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