ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

BMC Bioinformatics

Table 4 Overlap and semantic similarity analyses between the ROCS and BioGRID lists of uniquely identified Specific Prey Proteins in all bait experiments

Bait Experiment	ROCS Unique Prey Proteins (N^B)	ROCS Unique Specific Prey Proteins(S^B)	BioGRID Unique Specific Prey Proteins(B)	BioGRID Intersection (X)	BioGRID Intersection Significance (p-value)	BioGRID Semantic Similarity (sim_Res(c₁, c₂))
						BP	MF	CC
STK24	824	112	40	16	1.47041e-05	1.000	0.789	0.853
PPM1B	965	76	20	4	4.92866e-02	0.939	0.730	0.810
NME2	1349	260	26	18	2.58102e-08	0.939	1.000	0.937
CTNNBIP1	1229	69	13	6	3.00192e-05	0.939	1.000	1.000
VHL	5398	43	181	18	3.46865e-16	0.878	0.873	0.874

Hypergeometric test rejection probabilities (p-values) are given as well as protein lists semantic similarities for each gene ontology (Biological Process (BP), Molecular Function (MF), and Cellular Component (CC)). ROCS lists are reported for C − score C_S > Ĉ_S^cutoffand the marginal inclusion probability thresholds ${\tilde{p}}_{min}^{C}$ and ${\tilde{p}}_{min}^{B}$ as determined in each AP-MS experiment.

ISSN: 1471-2105