Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

Durek, Pawel; Schudoma, Christian; Weckwerth, Wolfram; Selbig, Joachim; Walther, Dirk

doi:10.1186/1471-2105-10-117

Table 3 Prediction Performance as measured by accuracy, sensitivity (sn), and specificity (sp)

From: Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

Kinase family	Kinase group	N	Sequence-only	Spatial- information enriched	NetPhos 3.1b	Disphos 1.3	KinasePhos 2.0
Ser kinases	/	363	0.69 ± 0.01 sn:0.76 ± 0.02 sp:0.62 ± 0.03	0.73 ± 0.01 sn:0.73 ± 0.01 sp:0.73 ± 0.02	0.64 ± 0.01 sn:0.70 ± 0.00 sp:0.58 ± 0.01	0.68 ± 0.01 sn:0.47 ± 0.00 sp:0.88 ± 0.03	0.50 ± 0.00 sn:1.00 ± 0.00 sp:0.50 ± 0.00
PKA	AGC I	34	0.83 ± 0.03 sn:0.93 ± 0.05 sp:0.83 ± 0.07	0.88 ± 0.02 sn:0.86 ± 0.05 sp:0.80 ± 0.07	0.82 ± 0.02 sn:0.82 ± 0.00 sp:0.81 ± 0.05		0.71 ± 0.03 sn:0.65 ± 0.00 sp:0.75 ± 0.04
PKC	AGC II	31	0.82 ± 0.02 sn:0.76 ± 0.03 sp:0.87 ± 0.03	0.82 ± 0.02 sn:0.80 ± 0.03 sp:0.81 ± 0.04	0.72 ± 0.02 sn:0.58 ± 0.00 sp:0.86 ± 0.04		0.64 ± 0.03 sn:0.61 ± 0.00 sp:0.66 ± 0.04
MAPK	CMGC II	12	0.89 ± 0.04 sn:1.00 ± 0.00 sp:0.79 ± 0.08	0.89 ± 0.04 sn:0.88 ± 0.15 sp:0.79 ± 0.08	0.69 ± 0.02 sn:0.42 ± 0.00 sp:0.96 ± 0.04		0.61 ± 0.05 sn:0.50 ± 0.00 sp:0.64 ± 0.08
CKII	CMGC IV	19	0.70 ± 0.03 sn:0.79 ± 0.18 sp:0.60 ± 0.18	0.74 ± 0.04 sn:0.88 ± 0.15 sp:0.61 ± 0.14	0.74 ± 0.02 sn:0.53 ± 0.00 sp:0.94 ± 0.04		0.62 ± 0.03 sn:0.47 ± 0.00 sp:0.67 ± 0.07
Thr kinases	/	134	0.68 ± 0.01 sn:0.55 ± 0.04 sp:0.87 ± 0.04	0.69 ± 0.01 sn:0.61 ± 0.04 sp:0.80 ± 0.04	0.63 ± 0.01 sn:0.49 ± 0.00 sp:0.77 ± 0.02	0.66 ± 0.03 sn:0.49 ± 0.00 sp:0.83 ± 0.05	0.50 ± 0.00 sn:1.00 ± 0.00 sp:0.50 ± 0.00
Tyr kinases	/	253	0.65 ± 0.01 sn:0.67 ± 0.06 sp:0.63 ± 0.06	0.67 ± 0.01 sn:0.51 ± 0.03 sp:0.81 ± 0.03	0.62 ± 0.01 sn:0.54 ± 0.00 sp:0.71 ± 0.01	0.53 ± 0.02 sn:0.29 ± 0.01 sp:0.77 ± 0.05	0.50 ± 0.00 sn:1.00 ± 0.00 sp:0.50 ± 0.00
SRC	PTK I	24	0.70 ± 0.03 sn:0.74 ± 0.15 sp:0.66 ± 0.16	0.75 ± 0.03 sn:0.77 ± 0.09 sp:0.72 ± 0.10	0.57 ± 0.01 sn:0.17 ± 0.00 sp:0.98 ± 0.10		0.70 ± 0.04 sn:0.83 ± 0.00 sp:0.66 ± 0.04
unspecific predictor		750	0.66 ± 0.01 sn: 0.65 ± 0.01 sp:0.69 ± 0.02	0.69 ± 0.01 sn:0.60 ± 0.03 sp:0.78 ± 0.03	0.63 ± 0.01 sn:0.61 ± 0.01 sp:0.66 ± 0.01	0.62 ± 0.01 sn:0.42 ± 0.01 sp:0.83 ± 0.03	0.50 ± 0.00 sn:1.00 ± 0.00 sp:0.50 ± 0.00

Results from the cross-validation of the various prediction approaches. The sequence-only and Spatial-information enriched methods were developed as part of this study and compared to to NetPhos 3.1b that includes the kinase-specific predictor NetPhos/K, Disphos1.3 and KinasePhos2.0. The size of the negative set was adjusted to the size of the positive sites, ensuring equal sizes of the sets and a comparison to original reports of accuracies of alternative prediction approaches. In the case of the kinase unspecific prediction of KinasePhos2.0, all sites were predicted to be phosphorylated by at least one kinase. Best performing methods are printed in bold-face. Sn denotes sensitivity, while sp denotes the specificity for the stated accuracy.

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