Functional Network of the Mitochondrial System

<div><p>(A) Full network containing 9,780 association lines connecting 876 protein nodes. Lines are shaded by the degree of STRING confidence in the association. Nodes are colored according to the following: known mitochondrial-localized proteins (reference set) correctly predicted by the linear classifier, green; known mitochondrial-localized proteins not captured by the linear classifier, light green; predicted proteins not annotated as mitochondrial-localized (mitochondrial candidates), orange; proteins predicted as additional interactors by the network (interactor candidates), blue; mitochondrial candidates recently annotated as mitochondrial-localized (MitoP2 database) or verified by mitochondrial import assay, red.</p><p>(B) Module map of 46 modules with five or more proteins. Modules were named and localized based on GO terms, with the following abbreviations: asm, assembly; biogen, biogenesis; cyt, cytoplasmic; dehy, dehydrogenase; met, metabolism; mito, mitochondrial; org, organization; proces, processing; syn, synthesis. The localization of modules in three different compartments—nucleus, mitochondria, and cytoplasm—is indicated by sectors of different colors. When the module contains a mixture of proteins with different localization it is annotated as shared between the different compartments. Module shared between mitochondria and nucleus or mitochondria and cytoplasm belong to green and yellow sectors, respectively. Cytoplasm refers to all of the contents of a cell excluding mitochondrion and nucleus but including the plasma membrane and other sub-cellular structures. The identity of all proteins and their functional links can be found in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020170#pgen-0020170-sg004" target="_blank">Figure S4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020170#pgen-0020170-sg005" target="_blank">Figure S5</a> for (A and B), respectively, where the standard gene names are shown within the nodes and are hyperlinked to STRING.</p>