Table 5

Overlap and semantic similarity analyses between the ROCS’s lists of Specific Prey Proteins with those obtained by SAINT and ComPASS in all bait experiments (see also Additional file 5: Table S3)
Bait Experiment ROCS Unique Prey Proteins (NB) ROCS Unique Specific Prey Proteins (SB) SAINT Unique Specific Prey Proteins (B) SAINT Intersection (X) SAINT Intersection Significance (p-value)

SAINT Semantic Similarity

(simRes(c1, c2))

BP MF CC
STK24 824 112 94 26 1.49146e-05 1.000 1.000 0.853
PPM1B 965 76 86 17 4.62432e-05 0.939 0.936 0.823
NME2 1349 260 210 47 1.25292e-2 1.000 1.000 0.937
CTNNBIP1 1229 69 161 8 1.45195e-1 1.000 0.873 0.937
VHL 5398 43 2 2 5.08701e-05 0.661 0.442 0.307
Bait Experiment ROCS Unique Prey Proteins (NB) ROCS Unique Specific Prey Proteins (SB) ComPASS Unique Specific Prey Proteins (B) ComPASS Intersection (X) ComPASS Intersection Significance (p-value)

ComPASS Semantic Similarity

(simRes(c1, c2))

BP MF CC
STK24 824 112 169 90 4.34990e-57 1.000 1.000 1.000
PPM1B 965 76 159 54 1.07087e-31 1.000 1.000 1.000
NME2 1349 260 242 162 2.50264e-87 1.000 1.000 0.937
CTNNBIP1 1229 69 146 44 2.00480e-27 1.000 1.000 1.000
VHL 5398 43 740 31 2.01445e-20 0.878 0.873 0.823

Using a similar overlap analysis by means of the hypergeometric distribution test and GO semantic similarity as in Table 4, we determined the statistical significance of the overlap between: (Top ) ROCS vs. SAINT, and (Bottom) ROCS vs. ComPASS for all gene ontologies (Biological Process (BP), Molecular Function (MF), and Cellular Component (CC)) and in all bait experiments. SAINT and ComPASS lists are reported for PSAINT > 0 and D − score > 0 respectively. ROCS lists are reported for C − score CS > ĈScutoffand the marginal inclusion probability thresholds <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/128/mathml/M249','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/128/mathml/M249">View MathML</a> and <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/128/mathml/M250','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/128/mathml/M250">View MathML</a> as determined in each AP-MS experiment.

Dazard et al.

Dazard et al. BMC Bioinformatics 2012 13:128   doi:10.1186/1471-2105-13-128

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