Extending signalling pathways with protein-interaction networks. Application to apoptosis.

Experimental expansion network

Here we present numerical results for Experimental expansion network. In the following sections we provide the numerals we used to compute the p-Value for our predictions. For the computation of p-Value we consider as candidates the set of nodes in the network with sensitivity higher than 95% and PPV above 90% in the 5-fold cross-validation assay. For each validation set we compute a p-Value describing the likelyhood of obtaining the subset of validated candidates from the total number of proteins in the network according to the sizes of the candidates set and the validation set. Thus, a different p-Value is obtained for each validation set (Keyword, ProMiner).

• Individual scoring methods
• Cumulative combinations
• All Vs all combinations

Individual scoring methods

Validation of candidates posed by each scoring method. First column shows the analyzed scoring method. Second column corresponds to the number of nodes that accomplished quality criteria in the requested scoring methods. Columns 3 to 5 show relevant parameters for Keyword validation: the number of validated candidates, the size of the validation set and the p-Value obtained. Columns 6 to 8 contain analogous information for ProMiner validation.

Scoring method	Number of candidates	Keyword validated candidates	Keyword validation size	Keyword validation p-Value	ProMiner validated candidates	ProMiner validation size	ProMiner validation p-Value	JEV mean	JEV differences p-Value
FF	1056	140	523	1.242032e-66	65	273	2.461601e-28	7.946040e+00	1.323286e-01
iALD	922	123	523	4.490711e-59	46	273	4.903930e-17	7.330094e+00	5.587686e-04
ALD	6179	192	523	6.395490e-08	77	273	1.208459e-01	6.820165e+00	5.565842e-95

The relevance of sequence similarity between interologs is analyzed in orthology expanded networks by removing those predictions that do not achieve a certain JEV value. Tables corresponding to the orthology filtered versions of this network are available for several -log(JEV) filter thresholds.
To access the tables, follow links below:

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Cumulative combinations

Validation of candidates posed by all possible combinations of N scoring methods, where N is shown in the first column. Second column corresponds to the number of nodes that accomplished quality criteria in the requested scoring methods. Columns 3 to 5 show relevant parameters for Keyword validation: the number of validated candidates, the size of the validation set and the p-Value obtained. Columns 6 to 8 contain analogous information for ProMiner validation.

Number of scoring method	Number of candidates	Keyword validated candidates	Keyword validation size	Keyword validation p-Value	ProMiner validated candidates	ProMiner validation size	ProMiner validation p-Value	JEV mean	JEV differences p-Value
3	91	23	523	2.415154e-49	7	273	1.010036e-15	3.333333e-01	7.853059e-72
2	552	97	523	1.266828e-125	42	273	1.864740e-54	1.223854e+00	1.746719e-279
1	6887	254	523	3.088208e-66	107	273	1.026741e-28	6.004628e+00	1.776595e-245

The relevance of sequence similarity between interologs is analyzed in orthology expanded networks by removing those predictions that do not achieve a certain JEV value. Tables corresponding to the orthology filtered versions of this network are available for several -log(JEV) filter thresholds.
To access the tables, follow links below:

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All Vs all combinations

Validation of candidates posed by each combination of scoring methods. Columns contain relevant parameters for the computation of the p-Value. For each validation method these are: number of candidates posed by the combination of scoring mehtods, number of validated candidates and the p-Value itself. The relevant fields of each validation method are colored in green if the row corresponds to the best combination of scoring methods for the validation method. For best combination of scoring methods rows, links lead to the details of validated protein candidates (under validated candidates columns) or to the details of new protein candidates (under combination of scoring methods column). Signalling-related functions of candidates from best combinations of scoring methods are given in Supplementary table 2.

Combination of scoring methods	Number of candidates	Keyword validated candidates	Keyword validation size	Keyword validation p-Value	ProMiner validated candidates	ProMiner validation size	ProMiner validation p-Value	JEV mean	JEV differences p-Value
ALD, FF	223	31	523	4.150866e-53	14	273	1.356413e-24	8.147472e-01	9.525647e-131
ALD, iALD	178	29	523	9.139749e-53	10	273	6.181775e-19	1.304365e+00	5.625477e-78
FF, iALD	333	83	523	3.251012e-127	32	273	6.093618e-49	9.538462e-01	2.078978e-222
ALD, FF, iALD	91	23	523	2.415154e-49	7	273	1.010036e-15	3.333333e-01	7.853059e-72

The relevance of sequence similarity between interologs is analyzed in orthology expanded networks by removing those predictions that do not achieve a certain JEV value. Tables corresponding to the orthology filtered versions of this network are available for several -log(JEV) filter thresholds.
To access the tables, follow links below:

none

2

5

10

15

20

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