Table 5

Keyword recovery scores for the Operon method alone and in combination with the Rosetta Stone (RS), Phylogenetic Profile (PP), and conserved Gene Neighbor (GN) methods
Method
 Number of links between SWISS-PROT annotated proteins
 Keyword recovery %
 Maximum false positive fraction
 Keyword recovery of random links (100 trials) %
 Random links SD %
 Keyword recovery signal to noise
0 bp Operon
 308
 51
 0.25
 5.6
 1
 9.1
25 bp Operon
 642
 49
 0.28
 5.6
 0.7
 8.8
50 bp Operon
 818
 47
 0.31
 5.7
 0.6
 8.2
75 bp Operon
 912
 44
 0.36
 5.5
 0.5
 8
100 bp Operon
 1044
 45
 0.35
 5.7
 0.5
 7.9
100 bp Operon and RS
 88
 67
 0.05
 5.5
 1.8
 12
100 bp Operon and GN
 638
 60
 0.16
 5.5
 0.7
 11
100 bp Operon and PP
 268
 62
 0.11
 5.8
 0.9
 11
100 bp Operon, PP and GN
 242
 61
 0.11
 5.6
 1.2
 11
100 bp Operon, PP and RS
 62
 74
 0.03
 5.6
 2
 13
100 bp Operon, RS and GN
 78
 65
 0.05
 6.3
 1.9
 10
All four methods
 54
 70
 0.04
 5.7
 2.3
 12

Keyword recovery and maximum false positive fraction calculated as described in Table 2. Random links were established between the same number of random pairwise Swiss-Prot annotated genes as exist real links between Swiss-Prot annotated genes (mean and standard deviation of 100 random trials indicated).

Signal to Noise calculated as:

Strong et al. Genome Biology 2003 4:R59   doi:10.1186/gb-2003-4-9-r59

Open Data