Protein complex analysis
To predict the most
important protein
complexes, protein–protein interactions for differentially expressed
TFs (DE-TFs) were retrieved from STRING database (Szklarczyk et al.,
2019). These interactions were filtered
by transcriptomic data
to keep only meaningful interactions. Finally these interactions along
with expression data were loaded into the cystoscope software (Saito et
al., 2012) and a protein–protein interaction network was constructed.
This network was analyzed by MCODE software (Bader & Hogue, 2003) in
the Cytoscape software environment. Complexes with scores more than two
were considered as significant protein complexes.