assessing the functional coherence of modules found in multiple-evidence networks from arabidopsis评估模块的功能一致性中发现一些网络从拟南芥.pdfVIP

Lysenko et al. BMC Bioinformatics 2011, 12:203 /1471-2105/12/203 RESEARCH ARTICLE Open Access Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis 1,2* 1 1 1 2 Artem Lysenko , Michael Defoin-Platel , Keywan Hassani-Pak , Jan Taubert , Charlie Hodgman , Christopher J Rawlings1 and Mansoor Saqi1 Abstract Background: Combining multiple evidence-types from different information sources has the potential to reveal new relationships in biological systems. The integrated information can be represented as a relationship network, and clustering the network can suggest possible functional modules. The value of such modules for gaining insight into the underlying biological processes depends on their functional coherence. The challenges that we wish to address are to define and quantify the functional coherence of modules in relationship networks, so that they can be used to infer function of as yet unannotated proteins, to discover previously unknown roles of proteins in diseases as well as for better understanding of the regulation and interrelationship between different elements of complex biological systems. Results: We have defined the functional coherence of modules with respect to the Gene Ontology (GO) by considering two complementary aspects: (i) the fragmentation of the GO functional categories into the different modules and (ii) the most representative functions of the modules. We have proposed a set of metrics to evaluate these two aspects and demonstrated their utility in Arabidopsis thaliana. We selected 2355 proteins for which experimentally established protein-protein interaction (PPI) data were available. From these we have constructed five relatio