Here we provide details about our default protein-protein interaction networks and the method definitions and PSI-MI codes used
to filter protein interaction databases during the data collection process:
TopoGSA protein interaction networks - overview:
Human (comprehensive) - 38857 interactions between 9392 proteins
Human (only proteome-scale 2-hybrid protein-protein interactions) - 2750 interactions between 5621 proteins
Yeast (S. cerevisiae) - 30420 interactions between 5246 proteins
Fly (D. melanogaster - 38500 interactions between 10563 proteins
Plant (A. thaliana) - 3663 interactions between 1731 proteins
Worm (C. elegans) - 5580 interactions between 3067 proteins
Method definitions and PSI-MI codes used to filter protein interactions:
Below we provide the complete list of method definitions and PSI-MI codes used during the construction of the above networks from public databases
to extract only direct binary protein-protein interactions and filter out all other indirect interaction types (some interaction databases do not provide PSI-MI codes but only a method definition, which was used instead for filtering):
beta lactamase complementation MI:0011
bimolecular fluorescence complementation MI:0809
biochemical MI:0401
Biochemical Activity
bioluminescence resonance energy transfer MI:0012
blue native page MI:0276
circular dichroism MI:0016
classical fluorescence spectroscopy MI:0017
Co-crystal Structure
competition binding MI:0405
confocal microscopy MI:0663
cross-linking studies MI:0030
dihydrofolate reductase reconstruction MI:0111
dynamic light scattering MI:0038
electron microscopy MI:0040
electron paramagnetic resonance MI:0042
electron resonance
electron tomography MI:0410
elisa: enzyme-linked immunosorbent assay
enzymatic studies MI:0415
enzyme linked immunosorbent assay MI:0411
Far Western
far western blotting MI:0047
filamentous phage display MI:0048
fluorescence microscopy MI:0416
fluorescence polarization spectroscopy MI:0053
fluorescence technologies MI:0051
fluorescence-activated cell sorting MI:0054
fluorescent resonance energy transfer MI:0055
FRET
green fluorescence protein complementation assay MI:0229
in-gel kinase assay MI:0423
ion exchange chromatography MI:0226
isothermal titration calorimetry MI:0065
lambda phage display MI:0066
lambda repressor two hybrid MI:0655
light scattering MI:0067
methyltransferase assay MI:0515
nuclear magnetic resonance MI:0077
PCA
peptide array MI:0081
phage display MI:0084
phosphatase assay MI:0434
protease assay MI:0435
protein array MI:0089
protein complementation assay MI:0090
protein cross-linking with a bifunctional reagent MI:0031