Table 2

EGF/ERK signal flow in the HPPI2 network. Proteins in the EGF-responsive phosphoprotein data set were mapped to first-, second-, and third-degree neighbors of the EGF/ERK core pathway. The proteins were further grouped into input or output neighbors on the basis of the edge direction relative to the core pathway. For each set of neighbors, the total number of nodes (neighborhood size) and number of mapped proteins were computed. We generated 1000 random sets with the same number of nodes as the respective neighborhood size. Enrichment was measured by comparing the data sets of associated proteins with the 1000 equal-size random sets of simulated interacting proteins (P < 0.05). The mean, SD, and P values were calculated on the basis of the overlap within each random set.

Data setDegree of
separation
Input neighborsOutput neighbors
Neighbor
size
Phospho-
proteins
Random
mean ± SD
PNeighbor
size
Phospho-
proteins
Random
mean ± SD
P
EGF-responsive
phosphoproteins
(327 proteins)
First4242622 ± 4.30.214363923 ± 4.4<0.001
Second187510296 ± 7.90.251963121102 ± 8.30.016
Third2254123116 ± 8.20.22116229084 ± 7.60.274