Table 1

Overview of seven Y2H and five AP-MS experiments
Reference
 VB
 CB
 TB
 VP
 VBP
 VBP/BP
 TI
 TI/VB
 REC
 UNR
Ito et al. [1]
 1,522
6,604
 2,493
 773
 0.51
 4,524
 3.0
 75
 803
Cagney et al. [2]
 19
31
 40
 11
 0.58
 54
 2.9
 3
 4
Tong et al. [3]
 20
22
 59
 5
 0.25
 115
 5.8
 1
 1
Hazbun et al. [4]
 66
100
 1,940
 28
 0.42
 2,524
 38
 4
 13
Zhao et al. [5]
 1
1
 90
 0
 0.00
 90
 90
 0
 0
Uetz et al. Experiment 1 [6]
 508
6,604
 630
 142
 0.28
 952
 1.9
 10
 47
Uetz et al. Experiment 2 [6]
 139
192
 400
 36
 0.26
 524
 3.8
 18
 7
Gavin et al. [7]
 455
 600
 725
 1,179
 271
 0.60
 3,419
 7.5
 192
 314
Ho et al. [8]
 493
 589
 1,739
 1,316
 231
 0.47
 3,687
 7.5
 69
 297
Krogan et al. [9]
 153
 165
 165
 483
 151
 0.99
 1,132
 7.4
 89
 157
Gavin et al. [10]
 1,752
 1,993
 6,466
 1,790
 991
 0.57
 19,105
 10.9
 1,077
 4,297
Krogan et al. [11]
 2,264
 2,357
 4,562
 5,323
 2,226
 0.98
 63,360
 28.0
 1,969
 34,363

VB, the number of viable baits; CB, the number of cloned (hybridized) baits, if available; TB, the total number of baits that the experimenters were initially aiming at; VP, the number of viable prey; VBP, the number of proteins observed as both bait and prey; TI, the total number of interactions observed; REC, the number of reciprocated interactions between proteins that were observed as both bait and prey; UNR, the number of unreciprocated interactions between proteins that were observed as both bait and prey. Not all of the experiments were genome-wide - some were focused on particular aspects of the cellular machinery [2-5,9]. Even in the so-called genome-wide studies [1,6-8,10,11], however, the viable baits cover only around a third of the yeast genes. This means that the largest part of interaction space by far, containing interactions between proteins not used as baits, was not sampled in any of these experiments. We can also see that TI/VB, the average number of interactions per viable bait, varies markedly between experiments. In the more focused studies, this will certainly be a result of different criteria for the selection of baits. In the genome-wide screens it may indicate the application of different, experiment-specific cutoffs.

Gentleman and Huber Genome Biology 2007 8:112   doi:10.1186/gb-2007-8-10-112