Fig 1.
Heatmap constructed for the 100 eigengenes of the clusters and the 42 experimental variables recorded for Dhc across 47 experiments with varying conditions.
The heatmap is organized by the hierarchal clustering of both the variables (y-axis) and experiments (x-axis). Blue, white, and red indicate a negative, neutral, or positive microarray expression ratio (or low, mid, or high values for experimental variables), respectively. The variables are segregated into distinct blocks by introducing a white space between groups of variables that had distances greater than 0.9 × (maximum hierarchical distance).
Fig 2.
The SPINE (SParse eIgengene Network) inferred for the Dhc transcriptomic data (center gray area).
Experimental variables are represented as yellow nodes with a consistent size. The size of a transcript cluster node is a function of the number of transcripts in that cluster, and these transcript cluster nodes are colored as either white to red or white to blue. The nodes are colored based on the proportion of their constituent transcripts that are RDase-related (with white and red indicating a lower and higher proportion, respectively) or the proportion of their constituent transcripts identified as other oxidoreductases putatively involved in electron transport (with white and blue indicating a lower and higher proportion, respectively). Both filters are considered simultaneously, allowing purple nodes. The network was visualized in Cytoscape v. 3.0. Red arrows highlight a zoomed in neighborhood view of two clusters that are discussed in the text: (left) members of and neighbors to the C27 eigengene, the cluster containing the most highly-expressed RDase tceA (DET0079); and (right) members of and neighbors to the C9 eigengene, the only cluster connected to the solvent toxicity (saturation) experimental condition in the model.
Fig 3.
The response of selected Dhc strain 195 transcripts to solvent toxicity.
(a) A line plot of the concentrations of PCE, TCE, DCE, VC, and ETH during the continuously fed experiment for the saturated (solid lines) and control (dashed lines) cultures. The biological duplicates are presented individually. Excess PCE was spiked into the experimental cultures at 24 hours. TCE and DCE levels were always below 5 µmol/L. (b) A line-plot of the transcript copies per mL of culture presented on a log scale for DET0097 (a putative regulator), DET0110 (hup hydrogenase large subunit), DET0137 (a putative methylglyoxal synthase), and 16S rRNA. Data for the saturated and control cultures are represented by solid and dashed lines, respectively.