| E Iy_s E_1 E E DRM cyt c nggTN c SCF PTN F NF F NF F NF F NF P1M FYN '-WB: *“’ ' 0 ~ - -° LYN?” FYN PTN G 8 O . O o . ' _ ‘—§ 8 2 O _ _ c ° to o - g o LYN .E V '5 o - . - - -PTN g N 3 o H FYN PTN FYN SCF LYN PTN LYN SCF <0 a) l!) U) : <1-(5 .C on U 2 ~ ii Iii lili i ills i q I | (G) Box plot shows amounts of FYN (red) and LYN (blue) in detergent-resistant (DRM) and-soluble (P1 M) fractions under control, ALK- or KIT-stimulated conditions as in A-D. (H) Bar plots show fold change (treatment/control if positive;-(treatment/contro|)‘1 if negative) in all cell fractions under unstimulated or stimulated conditions as in A-D. (G, H) Amounts of FYN and LYN in all cell fractions were quantified from 3—7 experiments; boxes show quartiles and whiskers show ranges in G, error bars are SEM in H. |
| Supporting Information | Fold change in response to RT K stimulation or inhibition. |
| Supporting Information | Fold changes are graphed on a blue-yellow color heat map as in Fig 4. |
| Tyrosine Kinase Posphorylation in Response to RTK Stimulation | Fold change in response to RTK stimulation or inhibition. |
| Tyrosine Kinase Posphorylation in Response to RTK Stimulation | Phosphorylation sites represent the sum of all peptides surrounding that site; peptides whose conserved sequence is present in several proteins are indicated with multiple names, e.g., “FYN 420; LCK 394; SRC 419; YES1 426.” Fold changes are graphed on a blue-yellow color scale with blue representing a decrease, and yellow, an increase, compared to control (key). |
| Experimental Prediction of | The fold change of protein phosphorylation for each treatment condition was calculated in comparison to the respective control and between treatment conditions (Fig 3A). |
| Interaction graphs | To select the minimal model structures, we used the discretized fold change (‘increase’, ‘decrease’, ‘no change’, ‘not conclusive’) of the phosphorylation state of two experimental conditions, C1 and C2. |
| Supporting Information | Fold change of protein phosphorylation states. |
| Supporting Information | For each protein, the fold change of the phosphorylation state measured by quantitative immunoblotting of two different experimental conditions is shown on a logarithmic scale at the indicated time points after 40 ng/ml of HGF stimulation. |
| Supporting Information | A) Fold change of Akt phosphorylation on threonine 308 and the active, not phosphorylated, SOS is shown (representative blot shown in SlA Fig) B) Fold change of the phosphorylation state of the indicated proteins upon PI3K inhibitors treatment. |
| Validation | Deleting T Fs that form cooperative logic gates gives rise to significantly higher fold changes of target gene expression. |
| Validation | The yeast TF knockout experiments give information regarding fold changes in gene expression as a result of deleting a single TF [31,32]. |
| Validation | For example, in analyzing 871 AND-gate-consistent triplets, we found that deleting either of their TFs gave rise to substantial down-regulation of their target genes, i.e., the logarithm expression fold changes were significantly less than zero (t-test p-value = 0.068). |