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Figure 4 | BMC Systems Biology

Figure 4

From: The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti

Figure 4

The Symbiosis Interactome network and its organization into functional modules. (A) Network visualization of the 440 proteins (nodes) and 1,041 interactions (edges) potentially involved in the S. meliloti-Legume symbiosis. The colours of each protein indicate the stage of symbiosis [see Additional file 2] or the phenotypic profile categories the proteins belong to (see panel). Edges are coloured according to the probability of interaction, from blue (less probability) to red (more probability). We used Biolayout [66] for network visualization. (B) Graphical overview of the interconnected functional modules predicted over the Symbiosis Interactome network presented in (A). Larger pie charts (blue sky colour) represents individual functional modules (only modules with 3 or more proteins are shown) and smaller pie charts represents proteins not predicted to be part of functional modules and directly interacting with modules, and coloured as in (A). Module borders are coloured if >60% of their members are associated with a single COGs category (black otherwise)(see panel). We used Cytoscape [67] for network visualization. COGs codes are as follow: [J] Translation, ribosomal structure and biogenesis; [A] RNA processing and modification; [K] Transcription; [L] Replication, recombination and repair; [B] Chromatin structure and dynamics; [D] Cell cycle control, cell division, chromosome partitioning; [Y] Nuclear structure; [V] Defense mechanisms; [T] Signal transduction mechanisms; [M] Cell wall/membrane/envelope biogenesis; [N] Cell motility; [Z] Cytoskeleton; [W] Extracellular structures; [U] Intracellular trafficking, secretion, and vesicular transport; [O] Posttranslational modification, protein turnover, chaperones; [C] Energy production and conversion; [G] Carbohydrate transport and metabolism; [E] Amino acid transport and metabolism; [F] Nucleotide transport and metabolism; [H] Coenzyme transport and metabolism; [I] Lipid transport and metabolism; [P] Inorganic ion transport and metabolism; [Q] Secondary metabolites biosynthesis, transport and catabolism; [R] General function prediction only; [S] Function unknown; [-] Non-annotated genes.

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