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Figure 3B shows parts of the thresholded PIP that are restricted to proteins with =20 inks (23), highlighting large complexes. Some predicted complexes overlap with the gold- standard positives (cytoplasmic ribosome) or the PIE (exosome, RNA polymerase I, 26S proteasome). Comparison with the gold- standard negatives showed where the PIP likely produced false complexes. Many protein asso- ciations only appear in the PIP and thus poten- tially represent new interactions and complex- es. An interesting example is the mitochondrial ribosome; it has appreciable overlap with both gold-standard positives and the PIE and con- tains plausible, newly predicted interactions with three proteins (/9).

Figure 3 B shows parts of the thresholded PIP that are restricted to proteins with =20 inks (23), highlighting large complexes. Some predicted complexes overlap with the gold- standard positives (cytoplasmic ribosome) or the PIE (exosome, RNA polymerase I, 26S proteasome). Comparison with the gold- standard negatives showed where the PIP likely produced false complexes. Many protein asso- ciations only appear in the PIP and thus poten- tially represent new interactions and complex- es. An interesting example is the mitochondrial ribosome; it has appreciable overlap with both gold-standard positives and the PIE and con- tains plausible, newly predicted interactions with three proteins (/9).

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We have thus far treated all interactions as independent. However, the joint distribution of interactions in the PIs can help identify large complexes: An ideal complex should be a “clique” in an interaction graph (1.e., a subgraph with MN — 1)/2 links between N proteins). One might ask whether simpler voting pro- cedures can match the performance of more The PIP had a higher sensitivity than the PIE for comparable TP/FP ratios (Fig. 2C). (“Sensitivity” measures coverage and is defined as TP/P, where P is the number of gold- standard positives.) Specifically, the sensitivity of the PIP is ~27% at our cutoff. This may seem low, but compares favorably with the PIE, which had a sensitivity of less than 1%. This means that we can predict, at comparable error levels, more complex interactions de novo than are present in the high-throughput experimental interaction data sets.
We have thus far treated all interactions as independent. However, the joint distribution of interactions in the PIs can help identify large complexes: An ideal complex should be a “clique” in an interaction graph (1.e., a subgraph with MN — 1)/2 links between N proteins). One might ask whether simpler voting pro- cedures can match the performance of more The PIP had a higher sensitivity than the PIE for comparable TP/FP ratios (Fig. 2C). (“Sensitivity” measures coverage and is defined as TP/P, where P is the number of gold- standard positives.) Specifically, the sensitivity of the PIP is ~27% at our cutoff. This may seem low, but compares favorably with the PIE, which had a sensitivity of less than 1%. This means that we can predict, at comparable error levels, more complex interactions de novo than are present in the high-throughput experimental interaction data sets.
Fig. 2. Comparison of PIP and PIE with each other and with the individual information sources. (A) The 7P/FP ratio as a function of Lo, for the PIP and the individual data from which it was computed. The ratio is computed as follows: ee a sa: ‘wees wecaok hismeeint
Fig. 2. Comparison of PIP and PIE with each other and with the individual information sources. (A) The 7P/FP ratio as a function of Lo, for the PIP and the individual data from which it was computed. The ratio is computed as follows: ee a sa: ‘wees wecaok hismeeint
[Nhp6 also binds DNA in competition with the nucleosome (28).] Our thresholded PIP and experimental data document a specific interaction between Nhp6A and Hhfl (H4), pinpointing the contact between the nucleo- some and Nhp6 to the H3-H4 heterodimer (Hhfl and Hhtl). This is plausible; because Nhp6 has been shown not to influence nu-
[Nhp6 also binds DNA in competition with the nucleosome (28).] Our thresholded PIP and experimental data document a specific interaction between Nhp6A and Hhfl (H4), pinpointing the contact between the nucleo- some and Nhp6 to the H3-H4 heterodimer (Hhfl and Hhtl). This is plausible; because Nhp6 has been shown not to influence nu-
The replication complex, a third experimen- tal validation of the PIP, assembles and dissem- bles from transiently interacting subcomplexes (e.g., MCM proteins, ORC, and polymerases) throughout the cell cycle (8, 30). Our predicted and experimentally verified interactions connect it, probably transiently, to another subcomplex, replication factor A (RFA, composed of Rfal, Rfa2, and Rfa3). Specifically, we predicted and verified interactions between RFA and two pro- teins associated with other replication subcom- plexes: Rfa2 with Top2 (a component of the nuclear synaptonemal complex) and Rfal with Pri2 (DNA polymerase a—primase subunit).
The replication complex, a third experimen- tal validation of the PIP, assembles and dissem- bles from transiently interacting subcomplexes (e.g., MCM proteins, ORC, and polymerases) throughout the cell cycle (8, 30). Our predicted and experimentally verified interactions connect it, probably transiently, to another subcomplex, replication factor A (RFA, composed of Rfal, Rfa2, and Rfa3). Specifically, we predicted and verified interactions between RFA and two pro- teins associated with other replication subcom- plexes: Rfa2 with Top2 (a component of the nuclear synaptonemal complex) and Rfal with Pri2 (DNA polymerase a—primase subunit).
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Bayesian NetworkLikelihood Functions
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