Research Paper Volume 15, Issue 2 pp 472—491

Figure 3. Correlation analysis of transcriptomics data. (A) The 7 color-coded modules (MEs, left side, Y-axis of heatmap), whose member genes are highly correlated over time, were analyzed for their correlation to each amino acid pool ((amino acids indicated on the X-axis, pool data are from [7]). The degree of correlation is indicated by the red-green (correlated-anticorrelated) scale at the right-side of the diagram and by numbers in columns which represent the correlation p-value and the correlation value (in parentheses). These values and the green highlighting indicate negative or anticorrelation: amino acid pools are small which transcripts are up-regulated, not down-regulated by Myr treatment. Additionally, the values in the column labeled 'InQ' represent the correlation between ME gene expression and the incubation time frame (1–6 hr) where the Turquoise module is the most correlated with time as shown graphically in panel F. The values in the column labeled 'myriocin' represent the association between ME gene expression and the absence/presence of myriocin where the no drug sample was set as 0 and the myriocin-treated sample was set as 1 for this calculation. This column indicates that the Green and Brown modules are the most anti-correlated (red shading) with amino acid pools, most of which are lowered by Myr treatment. (B) Network diagram showing the relationship of genes in the Green and Brown modules which are connected by genes in the Turquoise module. Genes are indicated by Nodes (circles) and relationships by edges. All genes and relationship values are presented in Supplementary Table 3. (C) Scatter plot of the Brown Eigengene across the 1–6 h time frame. (D) Enriched GO terms found in the Brown module. (E) Scatter plot of the Green Eigengene across the 1–6 h time. (F) Scatter plot of the Turquoise Eigengene across the 1–6 h time frame. (G) Enriched GO terms found in the Turquoise module. Genes used in calculating the mean Eigengene along with the 7 mean Eigengene values and their scatter plots are shown in Supplementary Table 3.