Environment and gene regulatory influence network for methanogenesis. (A) Environment and gene regulatory influence of methanogenesis biclusters is shown as a network diagram. One of the striking influences is the activation of three of the six methanogenesis related biclusters (bc_0009, bc_0019, and bc_0114) by MMP1100. H2 on the other hand, repressed bc_0009 and bc_0114. Regulatory influences of TFs and EFs on biclusters are associated with influence weight calculated by Inferelator. Influence weights can be used to filter most probable regulatory influences. For methanogenesis, network influences with weight less than 0.1 were not included in the analysis. Rectangles designate biclusters (colored the same as in Figs. 2, 3); circles denote transcription factors (red) and environmental factors (pale green); and triangles indicate AND logic gates of regulatory influences. Red arrows and green blunt-headed lines represent positive and negative influences, respectively, with their width being proportional to the influence weight. (B) The EGRIN model accurately recapitulates transcriptional changes within each bicluster, just from measured values of TFs and EFs. For selected biclusters, comparison of predicted mean expression values with the corresponding measured state is shown as line plots in the top panels. Prediction of the bicluster mean expression level in the time course conditions and steady-state conditions are shown as solid black and blue dashed lines, respectively. Corresponding measured expression is shown as dashed red lines. Correlation between predicted and measured relative transcript level changes for each bicluster is shown as a scatterplot in the bottom panels. Corresponding correlation coefficient is given at top, left and denoted by R.
