Fig. 3.

Heatmap of proteins significantly affected by disease treatment. Treatment effects were evaluated by pairwise comparisons of MS abundance data (log₂ summed ratios with imputation of missing values, FDR = 0.05) of different disease treatments within each animal replicate. Proteins were selected that had a differential effect of C or IC treatments and that were present in at least three time points across at least one consistent treatment condition between all three biological replicates (to avoid biases from imputing missing values), resulting in 188 selected proteins. The raw abundance value for each filtered protein was summed over all timepoints and log₂-transformed. For visualization, the log₂-transformed values were normalized via z-scoring across all treatment conditions, excluding injury alone and injury with Dex: control (N), cytokine (C), injury + cytokines (IC), Dex (D), cytokines + Dex (CD), and injury + cytokines + Dex (ICD). Proteins are plotted on the horizontal axis, and ordered based on their hierarchical clustering (Euclidian distance) across all six selected treatment conditions. Each individual replicate is plotted on the vertical axis, ordered by treatment condition and then by animal. The clustering reveals three major patterns of protein release: increased release by cytokines alone (↑Cyt), an increase by both cytokines and injury + cytokines (↑Cyt, ↑Inj + Cyt), and decreased release by cytokines and injury + cytokines (↓Cyt, ↓Inj + Cyt). These three patterns were used to designate the grouping categories in Table 1.