For the first top-level module spanning from reaction step 1 to 8, we perturbed seven forward kinetic parameters (k1, k2, k4, k5, k6, k7, and k8) and three kinetic parameters of reverse reactions (kr1, kr3, and kr7) while fixing the other parameters at their nominal values.
The gene membership of the module spanning more conditions is compared with that of modules spanning subsets of these time series.
The introductory lab module spans 8 wk, and the students are conducting a second laboratory module concurrently during the last 4 wk of the pClone module.
In this study, the module spanning fewer conditions was discarded if the overlap featured at least 50% of its gene members.
If the overlap is comparable with the size of the module spanning fewer conditions, then this module is discarded on the basis of it not contributing significant new information.
The promoters of two genes (At3g15210 and At5g05410) from a 26-gene module spanning B.cinerea infection and root and shoot responses to cold (Supplementary Fig. S4a) were screened against a TF library to identify TFs able to bind these DNA sequences.
For example, a researcher interested in unravelling shared regulatory networks between the biotic stress of B.cinerea infection and abiotic stress can see from Figure 5 that only one module spans B.cinerea infection, root response to drought and shoot response to cold.
In a 38-gene module spanning senescence and the root response to drought (Supplementary Fig. S4b), the promoters of three genes (At1g19180, At1g80840 and At3g23250) were screened and were bound by WRKY41, a member of the WRKY TF family (Eulgem et al., 2000).
We used a correlation threshold of 0.8, which needed to be fulfilled for each of the datasets the modules span.
CAT analysis using the assembled sequences (171,594 contigs) identified a total of 24,891 contigs (14.51% of total contigs) (Fig. 2) that had significant similarity with at least one of the reported CAZyme modules, spanning about 205 different CAZyme families (Additional file 1: Table S4).
