January 2011 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] figures
by Bram Slabbinck 28 Jan '11

28 Jan '11

Hi all, I am looking for some pictures for new.org stuff. If you think you have one or more nice/cool/superb/impressive/magnificent figures of a graph, network, genes, proteins, microarrays, spectrograms, etc. you can send it to me or put it in my PSB users folder. Preferably in vector format (eps, pdf)! thx a lot enjoy the weekend! Bram -- ========================================================= Bram Slabbinck, PhD Bioinformatics& Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be =========================================================

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[Beg-sysbiol] Abstract | A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation
by Klaas Vandepoele 23 Jan '11

23 Jan '11

*A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation* Nathaniel Robert Street, Stefan Jansson and Torgeir R Hvidsten BMC Plant Biology 2011, 11:13doi:10.1186/1471-2229-11-13 _Abstract_ Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species. We present a systems biology model of the regulatory network of Populus leaves. The network is reverse-engineered from promoter information and expression profiles of leaf-specific genes measured over a large set of conditions related to stress and developmental. The network model incorporates interactions between regulators, such as synergistic and competitive relationships, by evaluating increasingly more complex regulatory mechanisms, and is therefore able to identify new regulators of leaf development not found by traditional genomics methods based on pair-wise expression similarity. The approach is shown to explain available gene function information and to provide robust prediction of expression levels in new data. We also use the predictive capability of the model to identify condition-specific regulation as well as conserved regulation between Populus and Arabidopsis. We outline a computationally inferred model of the regulatory network of Populus leaves, and show how treating genes as interacting, rather than individual, entities identifies new regulators compared to traditional genomics analysis. Although systems biology models should be used with care considering the complexity of regulatory programs and the limitations of current genomics data, methods describing interactions can provide hypotheses about the underlying cause of emergent properties and are needed if we are to identify target genes other than those constituting the "low hanging fruit" of genomic analysis. Fulltext: http://www.biomedcentral.com/1471-2229/11/13 Note that N. Street is an invited speaker at the Comparative & Regulatory Genomics Conference <http://bioinformatics.psb.ugent.be/crg_event/conference/about> (April 2011, Ghent) kind regards, Klaas Vandepoele

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[Beg-sysbiol] A stele-enriched gene regulatory network in the Arabidopsis root
by Klaas Vandepoele 19 Jan '11

19 Jan '11

A stele-enriched gene regulatory network in the Arabidopsis root Siobhan M Brady^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1>, ^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Lifang Zhang^3 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a3> , Molly Megraw^4 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a4> , Natalia J Martinez^5 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a5> , Eric Jiang^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> , Charles S Yi^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> , Weilin Liu^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> , Anna Zeng^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Mallorie Taylor-Teeples^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Dahae Kim^2 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a2> , Sebastian Ahnert^6 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a6> , Uwe Ohler^4 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a4> , Doreen Ware^3 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a3>, ^7 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a7> , Albertha J M Walhout^5 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a5> & Philip N Benfey^1 <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#a1> <http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html#top>*Abstract* Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered. http://www.nature.com/msb/journal/v7/n1/full/msb2010114.html

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