Relationship between noise levels and RMSE.

<p>This chart shows the RMSE values for inferred transition matrices of n-39 network under 6 perturbations at different noise levels. The standard deviations of noises vary from 10 to 1. In Step 2, the RMSE values range from to ; in Step 3, the RMSE values range from to .</p

ROC curves of network structure inference.

<p>The performance of structure inference, under 6 different numbers of perturbations (from 2 to 7), is evaluated by ROC curves. Each subplot contains the inference results for 6 benchmark networks. The average AUROC is 0.97. More specifically, the maximum AUROC value 1.0 is achieved by the n-4 network (3–7 perturbations) and the n-11 network (6–7 perturbations), while the minimum AUROC value 0.88 is obtained by the n-58 network (2 perturbations).</p

Precision-recall curves of network structure inference.

<p>The performance of structure inference, under 6 different numbers of perturbations (from 2 to 7), is evaluated by Precision-recall curves. Each subplot contains the inference results for 6 benchmark networks. The average AUPR is 0.95. More specifically, the maximum AUPR value 1.0 is achieved by the n-4 network (3–7 perturbations) and the n-11 network (6–7 perturbations), while the minimum AUPR value 0.75 is obtained by the n-58 network (2 perturbations).</p

The process of refinement.

<p>The equations at the left and right side of arrows are original and reduced respectively. According to inferred transition matrix , there are two pathway and crosstalk between them. The species are silent, having no links with others. All elements associated with the silent species are removed from the transition matrix to form the refined transition matrix . All columns measuring the silent species are deleted from the measurement matrix to form the refined measurement matrix . The refined concentration vector, , only keeps the concentrations of active species (e.g., ). An element of the refined observation vector is equal to the corresponding element of the observation vector subtracted by the concentrations of the silent species involved in this measurement. If all species involved in a measurement are silent, simply remove this measurement.</p

Bar charts of RMSE for inferred transition matrices.

<p>These charts show the results of both Step 2 and Step 3 for 6 different benchmark networks with different numbers of perturbations varying from 2 to 7. In Step 2, the RMSE values range from to with the mean value of ; in Step 3, the RMSE values range from to with the mean value of . The RMSE ratios (Step 3/Step 2) vary from 0.14% to 51% with the mean value of 17%.</p

Sensitivity/specificity v.s. threshold parameter.

<p>These graphs show the relationships between sensitivity (above) and specificity (below) and threshold parameter for 6 different benchmark networks with different numbers of perturbations varying from 2 to 7. For , the average specificity is 0.9989 and the average sensitivity reaches its maximum value of 0.9453. When increases to , the average specificity is 0.9999 and the average sensitivity decreases to 0.8742. If increases to a relatively large value , the average specificity achieves 1.000 but the average sensitivity becomes 0.8188.</p

Characteristics of the benchmark network set.

<p>Characteristics of the benchmark network set.</p

Relationship between the average variance and RMSE.

<p>Each point represents an experiment for a benchmark network under a specific number of perturbations. For example, 2-n-53 means the experiment for n-53 network under 2 perturbations. The x-coordinate indicates the natural logarithm of the average variance for all elements in the refined transition matrix, while the y-coordinate indicates the RMSE values of the refined transition matrix. The RMSE values range from to and the average variance varies from to .</p

Additional file 2: of The anti-proliferative and anti-inflammatory response of COPD airway smooth muscle cells to hydrogen sulfide

Figure S2. Further examples of the effect of the H2S donor, NaSH on CBS and MPST protein expression, and activation of extracellular signal–regulated kinase (ERK)–1/2 and p38 mitogen-activated protein kinase (MAPK) in human ASM cells from non-smokers, smokers and COPD patients. ASM cells were incubated with FCS (2.5%) for 1 h and NaSH (100 μM) was added for another 24 h. CBS, MPST (A), Total and phospho–ERK-1/2, total and phospho-p38 and β-actin (B) were detected by Western blotting. (JPG 212 kb

Additional file 1: of The anti-proliferative and anti-inflammatory response of COPD airway smooth muscle cells to hydrogen sulfide

Figure S1. Immunohistochemistry staining of CSE, CBS and MPST in bronchial biopsies from non-smokers, smokers and COPD patients. Photomicrographs showing representative photomicrographs of cystathionine-γ-lysase (CSE), cystathionine-β-synthase (CBS) and 3-mercaptopyruvate sulphur transferase (MPST) staining in the bronchial mucosa from control non-smokers, control smokers with normal lung function and mild/moderate COPD patients. Immune-stained airway smooth muscle cells are indicated by brown staining. Results are representative of those from 13 non-smokers, 14 smokers with normal lung function, 15 mild/moderate COPD patients. Calibration bar represents 20 μm. Graphical representation of the results are shown in the right hand panels. (JPG 332 kb