It should also be noted that individual amino acids in the same group also show some variation in C2UR, these variations are represented as error bars in Supplementary Figure 6 (see Supplementary Figure 7 for the complete and individual results for representative amino acid, valine, from the case of MBP).
The contribution strengths for a subset of all contributing reactions is shown in Figure 5 (see Additional file 1: Text S1 Figure S3 for the complete set of contributions).
The reproducibly identified enhancers in proximity of induced genes correspond to binding sites of known macrophage TFs such as SREBF2, FLI1, CEBP-family and SPI1, as suggested by the de novo motif analysis of the underlying sequences for enriched motifs (Fig. 4b, see Additional file 1: Figure S4 for the complete list).
Among these gene pairs, we found that the GC content of the Arabidopsis homologs remains unimodal, as is shown for the full set Arabidopsis genes in Figure 1, whereas the content of the rice homologs remains bimodal, again as shown in Figure 1 for the complete rice data set.
As is illustrated in Figure 12, for the complete spatiotemporal synthesis, we apply our method and the method of Guo et al. [24] in cascade.
Refer to supplemental Table S6 and supplemental Figure S2 for the complete clfB data set.
Illustrated in Figure 3A are representative data from a single time point 8.5 hours after insulin stimulation (see Table S3 and Figure S2 for the complete data set).
Among those genes (see Figure S2 for the complete list) the ZEB1 transcription factor most clearly corresponded to morphology and strongly correlated with down regulation of the epithelial marker, E-cadherin (CDH-1) [7], [8], [9], [9] in the mesenchymal-like cells.
See Additional file 1: Figure S1 for the complete translation scheme.
Distributions of the most important network properties are plotted in Figure 5 for the complete (blue) metabolic network.
