[Beg-sysbiol] ENFIN-DREAM conference Madrid
Hi all, Just a few points to remember from the ENFIN-DREAM conference (<http://www.enfin.org/page.php?page=enfin_dream>) I attended this week: - ENFIN seems like a very succesful network: partners really share data and collaborate on various projects. If there's a successor to this project, we should try to be part of it. Let's get ourself known to these people, perhaps by inviting some for a seminar? - There will be a DREAM3 conference in Boston end of october/early november 2008. New challenges will also feature model based inference (predicting behavior of unseen data) which is good news for us. The conference will be organized back-to-back with a recomb sysbiol satellite meeting and another meeting organized by Manolis Kellis. - A few talks mentioned "method integration" as we have discussed here as well (to integrate results from enigma and lemone), so this is certainly a topic of interest right now. They used a simple approach of converting all predictions of different methods as p-values which can be combined in weighted sums by the method of <http://www.pnas.org/cgi/content/abstract/102/48/17296>. - Jaak Vilo talked about a method to predict new genes participating in known pathways by overlaying them with expression data (an extension of their tool KEGGanim <http://biit.cs.ut.ee/kegganim/>). They used a completely trivial method (pairwise Pearson correlations with genes in the pathway). I have the feeling it's very easy to improve by modeling the condition dependent expression of genes in a pathway using our tools and then compute the probability for new genes to belong to that pathway. This might be a good project for a new phd student, e.g. focused on combining our arabidopsis expression data with the pathways in reactome. Leuven is also interested in these kind of things. - For Sofie: do you know the BioCreative text mining competitions? <http://www.pdg.cnb.uam.es/BioLINK/BioCreative.eval.html> <http://biocreative.sourcefourge.net> Might be good to participate in the next one to promote genefetch. If you want to know more about specific talks, take a look at the program and ask me. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>
Tom Michoel wrote:
- Jaak Vilo talked about a method to predict new genes participating in known pathways by overlaying them with expression data (an extension of their tool KEGGanim <http://biit.cs.ut.ee/kegganim/>). They used a completely trivial method (pairwise Pearson correlations with genes in the pathway). I have the feeling it's very easy to improve by modeling the condition dependent expression of genes in a pathway using our tools and then compute the probability for new genes to belong to that pathway. This might be a good project for a new phd student, e.g. focused on combining our arabidopsis expression data with the pathways in reactome. Leuven is also interested in these kind of things.
I would like to add I am currently finalizing a study that a.o. estimates the prediction power of (simple global) coexpression information (including some T-DNA screens to evaluate some predictions). Methods like query-based biclustering approaches (using known genes as queries) indeed should yield better results than simple global measures, but in the end proving your predictions experimentally might be the real challenge. This paper - amongst others - /Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis/ was published this week in Plant Phys and does exactly the same think: linking unknown genes with known (e.g. pathway) genes using global expression similarity measures plus using differentially expressed signatures. Klaas
participants (2)
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Klaas Vandepoele -
Tom Michoel