Figure 1.
The BMSN and the LMSN networks.
We obtained a) the BMSN and b) the LMSN by choosing the edges of human PPI network with GUILD Score higher than 0.178. The proteins that have PDB structures are highlighted in pink, plus the edges that have complexes modeled by PRISM are also in pink color. c) PLOD2 cluster (the first-degree neighbors of PLOD2) from the BMSN d) BMSN and LMSN merged as a one big network. There are 84 common proteins and 71 common PPIs (blue edges). The edges that are only present in LMSN are shown with green and the edges that are only present in BMSN are shown with pink.
Figure 2.
The percentages of KEGG classes observed in LMSN and BMSN.
Figure 3.
Commonly observed interfaces of lung metastasis network.
In this figure structural sub-networks are also included. In these sub-networks only the interactions that have PRISM modeled complex structures are present. Each node represents a protein that has 3D structure and each edge stands for a distinct model between two proteins. The relevant template interfaces are represented with pink edges in these structural sub-networks.
Figure 4.
Commonly observed interfaces of brain metastasis network.
Legend for the sub-networks is the same as in Figure 3.
Figure 5.
Percentages of source organisms.
We considered the interfaces’ number of observations in the networks. 53% of the modeled complexes use microbial template interfaces in BMSN and this percentage is 59% in LMSN.
Figure 6.
The PRISM predictions for a) EREG (blue) – EGFR (pink), b) EREG (blue) – ERBB4 (green) interaction, c) HBEGF (purple) - EGFR (pink) interacrion and d) HBEGF (purple) – ERBB4 (green) interaction.
We have discovered multiple genetic variations happening on these interfaces.
Figure 7.
The PRISM predictions for ELANE (orange) - VCAM1 (green) and ELANE - CSF3 (blue) interaction.
The amino acids 98, 101, 126 (red amino acids) on ELANE have genetic variations. Amino acid 101 is a hotspot in the CSF3 – ELANE interface, moreover amino acids 98 and 126 are part of the ELANE – VCAM1 interface.