Subtracted interaction network of some nodes based on biological processes.

<p>MEA, DFR, JA, ABA, auxin, ethylene, SEC14, FAH and PR-4 formed an interconnected sub-network, while AHA10, FSD1, ATPDIL1-2 and AT4G20830 formed a separate, small sub-network. The network was visualized using Cytoscape software. Upregulated proteins are colored red, and downregulated proteins are colored green. The Excel file of the map can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049931#pone.0049931.s004" target="_blank">Table S4</a>.</p

Subtracted interaction network of several upregulated FG proteins based on biological processes.

<p>Relations between hubs of MEA, FAH1, PR-4, SEC14 and DFR are shown. upregulated and downregulated genes are shown in red and green respectively. Relations were extracted from the primary network using a language program “MATLAB”. Using language program, it was asked for all the interactions between MEA, SEC14, PR-4, DFR and FAH1 from network to predict which proteins or biological processes are affected by their interactions. As shown, MEA and PR-4 are linked to each other by proliferation process. FAH1 (involved in cell death program) is linked to plant defense through DFR and phenylpropanoid. But SEC14 was not connected to any of other four proteins.</p

Over-represented GO terms (“biological process” category) in the FG interaction network.

<p>Corrected p-values less than 5 E-5 were considered statistically significant.</p><p>An Excel file of all GO terms is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049931#pone.0049931.s006" target="_blank">Table S6</a>.</p

Interaction network of FG proteins based on molecular function.

<p>The network was visualized using Cytoscape software. upregulated proteins are indicated in red, and those that are downregulated are shown in green. Excel file of the map have been provided in Table S5.</p

Identification of essential proteins/hubs in the molecular function network using the BN and DSS methods.

<p>Figures A and B show the top 10 highest ranked hubs identified by BN and DSS methods, respectively. Red proteins are upregulated based on the microarray data.</p

Over-represented GO terms (“molecular function” category) in the FG interaction network.

<p>A corrected p-value less than 5E-2 was considered statistically significant. An Excel file of all GO terms is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049931#pone.0049931.s007" target="_blank">Table S7</a>.</p