a systems biology model of the regulatory network in populus leaves reveals interacting regulators and conserved regulation监管网络的系统生物学模型在杨树树叶显示交互监管者和守恒的监管.pdfVIP

Street et al. BMC Plant Biology 2011, 11:13 /1471-2229/11/13 RESEARCH ARTICLE Open Access A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation 1 1 1,2* Nathaniel Street , Stefan Jansson , Torgeir R Hvidsten Abstract Background: 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. Results: 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