  Living systems rely on coordinated molecular interactions, especially those
related to gene expression and protein activity. The Unfolded Protein Response
is a crucial mechanism in eukaryotic cells, activated when unfolded proteins
exceed a critical threshold. It maintains cell homeostasis by enhancing protein
folding, initiating quality control, and activating degradation pathways when
damage is irreversible. This response functions as a dynamic signaling network,
with proteins as nodes and their interactions as edges. We analyze these
protein-protein networks across different organisms to understand their
intricate intra-cellular interactions and behaviors. In this work, analyzing
twelve organisms, we assess how fundamental measures in network theory can
individuate seed-proteins and specific pathways across organisms. We employ
network robustness to evaluate and compare the strength of the investigated PPI
networks, and the structural controllability of complex networks to find and
compare the sets of driver nodes necessary to control the overall networks. We
find that network measures are related to phylogenetics, and advanced network
methods can identify main pathways of significance in the complete Unfolded
Protein Response mechanism.
