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Published online Oct 25, 2010. doi: 10.1371/journal.pone.0013606
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Figure 2
Understanding the dynamic programs that a yeast cell utilizes in response to the external stimulus of an antioxidant compound.
(A) The primary FA-specific protein-protein interaction (PPI) network (3,251 nodes, 12,462 edges) constructed by the list of the 64 genes that significantly responded to the FA environmental perturbation, independently of the aeration level, (B) High-scoring active modules identified in the primary FA-specific PPI network. Bold font indicates genes that belong to the list of the 64 genes, (C) The ACTMOD network, consisting of 167 nodes and 1,651 edges, using the “organic layout” in Cytoscape, (D) Sub-cellular localization of the 167 nodes of the ACTMOD network, (E) Functional enrichment (biological process, BP) of the ACTMOD network. For some nodes no functional annotation could be retrieved. During visualization feature assignment, color and shape codes have been defined as follows. Shape code: OCTAGON was used to indicate genes with significant differential expression in the (+)FA(+)O2 vs. (+)FA(−)O2 t-test, TRIANGLE for genes with significant differential expression in the (+)FA(−)O2 vs. (−)FA(−)O2 t-test, ROUND RECTANGULAR for genes with significant differential expression in the ANOVA statistic, and PARALLELOGRAM for genes with significant differential expression in the (+)FA(+)O2 vs. (−)FA(+)O2 and (+)FA(−)O2 vs. (−)FA(−)O2 t-tests. Color code: GREEN indicates down-regulation, while RED indicates up-regulation.
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