Figure 1.
Results of the benchmark studies for the individual prediction methods and the integrated methods.
A and C plots are from Yeast datasets and B and D are for Human results. A and B plots show precision versus p-values and C and D graphs show precision versus recall. Inset to the C plot shows an enlargement to visualize the improvements obtained by using the Fisher integration in yeast.
Figure 2.
Yeast degree distribution for the various networks analysed.
Panels A and B correspond to the KG and PG networks respectively, the legend for these panels show the correlation coefficients and exponents corresponding to the linear regression fit of the data. The corresponding randomised networks are shown below for KG (panels C, E) and PG (panels D, F) networks respectively. Panels C and D are from network randomisations by the adjacency method (see the section: Network randomisation). Panels E and F randomisations are from the evidence and p-value shuffling respectively.
Figure 3.
Human degree distribution for the various networks analysed.
Panels A and B correspond to the KG and PG networks respectively, the legend for these panels show the correlation coefficients and exponents corresponding to the linear regression fit of the data. The corresponding randomised networks are shown below for KG (panels C, E) and PG (panels D, F) networks respectively. Panels C and D are from network randomisations by the adjacency method (see the section: Network randomisation). Panels E and F randomisations are from the evidence and p-value shuffling respectively.
Table 1.
PG and KG networks intersection analysis.
Table 2.
Ten top proteins in the yeast and human PGki_er ranked lists.
Table 3.
Human PGki_er ranked list enrichment analysis in the GO database.
Figure 4.
PG networks functional context validation by the KG≥2 evidences dataset.
These plots present the precision value (y-axis) versus specific bits similarity score between the interaction profiles of the protein pairs (x-axis in plots A and C) and versus Recall (# of pairs predicted, x-axis in plots B and D) in yeast (plots A and B) and human (plots C and D) PG 0.001&0.0014 networks. The gold standard dataset used, KG≥2 evidences, is described in the section: Validation of the second order predictions for the PG networks.