Fig. 5. Systems biology approach with Nebula.

A Nebula employs a systems biology approach, presenting proteins differentially regulated for each study as networks, enabling a detailed exploration of shared proteins among groups (provided as a Source Data file). B Differentially regulated proteins can be compared pairwise using statistical tests or similarity indices, with a heatmap displaying each pairwise result. Users have the option to define background size or utilize all identified genes in all conditions as background for Fisher’s Test. Here, we performed Fisher’s exact test to compare groups using human proteome background length (20,423). C Based on results from similarity indices or Fisher’s Test, users can generate a network, establishing links between studies according to parameter thresholds.