Table 1. Head-to-head comparison of topological annotation methods.

We compared four methods including graph diffusion, betweenness centrality, first neighbors, and second neighbors. The table shows the number of statistically significant crosstalk proteins at the 0.05 and 0.01 levels. We show the number of significant proteins excluding seed proteins. Seed proteins are excluded because they were selected for this study. We show the significance of the enrichment in angiogenesis terms for the crosstalk proteins found using each method. The table also shows the number of GO term enrichments at the 0.01, 0.001, and 0.0001 levels.

Comparison Type	Graph Diffusion	Betweenness Centrality	First Neighbors	Second Neighbors
Proteins (p < 0.05) out of 13491	877	145	143	66
Proteins (p < 0.01)	398	87	69	44
Proteins (p < 0.01) & seed (out of 31)	10	5	7	10
GO enrichments (p < 0.01 )	117	90	57	40
GO enrichments (p < 0.001)	85	49	34	34
GO enrichments (p < 0.0001)	65	36	22	28