Table 3

The effect of normalization on the ranking.

Query Term
 Query Type
 Prominence Model
 Average No. Neighbors
 Average Consistent Neighbors
 Average Ratio
 Q(R)
 UROC (R)


Hubs & Authorities
 4.38
 0.6
 0.13
 167
 4879


Hubs & Authorities(N)
 7.64
 2.58
 0.52
 705
 23809
ubiquitin
 protein
 Eigenvector Centrality
 4.38
 0.6
 0.13
 167
 4879


Eigenvector Centrality(N)
 1.04
 0.9
 0.88
 307
 7871


PageRank
 12.18
 3.56
 0.27
 977
 26021


Hubs & Authorities
 1.19
 0.79
 0.48
 357
 10086


Hubs & Authorities(N)
 1.19
 0.79
 0.48
 357
 10112
stromelysin
 protein
 Eigenvector Centrality
 1.19
 0.79
 0.48
 357
 9912


Eigenvector Centrality(N)
 1.19
 0.79
 0.48
 357
 9057


PageRank
 1.19
 0.79
 0.48
 357
 11593


Hubs & Authorities
 5.22
 1.08
 0.25
 317
 6137


Hubs & Authorities(N)
 3.62
 1.2
 0.67
 372
 11947
cancer
 protein
 Eigenvector Centrality
 5.2
 0.9
 0.21
 245
 5346


Eigenvector Centrality(N)
 1.24
 0.98
 0.86
 321
 8137


PageRank
 6.68
 1.8
 0.30
 535
 16082


Hubs & Authorities
 1.1
 0.67
 0.58
 223
 4520


Hubs & Authorities(H)
 1.1
 0.67
 0.58
 223
 4345
autoimmune
 protein
 Eigenvector Centrality
 1.1
 0.67
 0.58
 223
 4520


Eigenvector Centrality(H)
 1.1
 0.67
 0.58
 223
 4830


PageRank
 1.1
 0.67
 0.58
 223
 4582

For each model we repeated the computations with the unnormalized and the normalized (N) matrices. See Table 2 for details.

Shafer et al. BMC Bioinformatics 2006 7:71   doi:10.1186/1471-2105-7-71