Figure 3

Gene coexpression network analysis. (a) The gene coexpression network. The 3,600 most varying genes were selected to construct a weighted gene coexpression network. I, The average linkage hierarchical clustering tree; II, clustered gene modules represented by different colors; III, gene significance of the individual modules. The green, brown and yellow modules were enriched in significant genes most highly correlated with the treatment conditions (p < 0.0001). Gene significance = -log (p value). IV, The synergistic gene enrichment. The mean synergistic indices (SI) of network genes that were upregulated by DEP, ox-PAPC and the corresponding combinatorial treatment of DEP plus ox-PAPC were calculated for each network module. The green, brown and yellow modules were also enriched in genes synergistically coregulated. Mean SI, mean synergistic index as defined in Materials and methods. (b) Heat map of the green module; (c) Heat map of the brown module. Expression levels of (b) 307 genes and (c) 426 genes are represented in the rows by color coding (green = low expression, red = high expression), in triplicate samples for each treatment condition (columns). Both modules show a clear synergistic/additive pattern where the combinatory treatments exhibited as a whole either a greater level of upregulation (towards red) in 274 genes (b) and 335 genes (c) at the top or downregulation (towards green) in 33 genes (b) and 91 genes (c) at the bottom, compared with the corresponding concentrations of DEP and ox-PAPC alone. Color scale is shown at the right of both heat maps, ranging from 0 (indicated by the green color at the bottom) to 1.0 (indicated by the red color at the top) as a reflection of the level of mRNA expression. DEP5 and DEP25, DEP 5 and 25 μg/ml, respectively; ox10, ox20, ox40: ox-PAPC 10, 20 and 40 μg/ml, respectively; DEP5 + (ox10, ox20 ox40): DEP 5 μg/ml + ox-PAPC 10, 20 and 40 μg/ml respectively.