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

STRING+ expansion network

Here we present numerical results for STRING+ 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 validationset 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
FF	1210	148	584	1.182081e-74	75	297	7.338670e-38	6.694502e+00	2.598739e-02
SC	10455	440	584	7.886991e-59	147	297	1.960715e-07	5.597573e+00	7.203347e-125
ALD	8539	317	584	4.794928e-33	131	297	8.343566e-09	3.797001e+00	< 1.000000e-323
iALD	1115	138	584	2.163702e-70	51	297	1.680312e-20	6.634734e+00	2.278887e-02

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 validationset of

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
4	82	24	584	1.370731e-55	15	297	6.687346e-35	5.000000e-06	2.798128e-68
3	307	55	584	2.422594e-92	37	297	3.577775e-62	3.943965e-01	4.084952e-181
2	5544	241	584	8.678039e-104	100	297	8.620752e-44	2.620291e+00	< 1.000000e-323
1	13719	542	584	1.720187e-73	184	297	7.695059e-26	4.367112e+00	< 1.000000e-323

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 2set of

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
SC, ALD	5068	166	584	2.678430e-77	83	297	2.296989e-39	2.810622e+00	< 1.000000e-323
SC, FF	302	46	584	1.509742e-77	40	297	1.805579e-67	5.556762e-01	3.453966e-184
SC, iALD	274	45	584	6.523748e-78	22	297	1.674821e-38	1.281023e+00	1.631619e-116
ALD, FF	252	40	584	7.788526e-71	33	297	1.620105e-58	3.449773e-01	6.163855e-166
ALD, iALD	186	37	584	7.454525e-71	15	297	3.033181e-29	4.268979e-01	7.959854e-94
FF, iALD	322	89	584	1.171110e-148	26	297	2.071618e-43	6.687911e-01	7.357233e-226
SC, ALD, FF	174	31	584	2.280242e-60	32	297	2.625004e-62	3.088564e-01	2.617585e-114
SC, ALD, iALD	140	31	584	1.315252e-63	15	297	3.579450e-31	3.225990e-01	3.943801e-76
SC, FF, iALD	135	35	584	1.729353e-72	20	297	1.466633e-41	1.515182e-01	1.125080e-109
ALD, FF, iALD	104	30	584	5.628178e-66	15	297	3.171190e-33	3.960396e-06	2.155594e-86
SC, ALD, FF, iALD	82	24	584	1.370731e-55	15	297	6.687346e-35	5.000000e-06	2.798128e-68

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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