PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship

Jung, Inkyung; Matsuyama, Akihisa; Yoshida, Minoru; Kim, Dongsup

doi:10.1186/1471-2105-11-S1-S10

BMC Bioinformatics

Table 3 Performance comparison with AutoMotif for 48 kinases.

From: PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship

Kinase	New method			AutoMotif			Kinase	New method			AutoMotif
	ACC	P	R	ACC	P	R		ACC	P	R	ACC	P	R
CDK_group(102)	0.93	0.57	0.85	0.94	0.80	0.46	Abl(48)	0.92	0.67	0.25	0.89	0.00	0.00
GSK-3_group(33)	0.91	0.56	0.15	0.91	1.00	0.03	PDK-1(35)	0.96	0.85	0.66	0.93	0.82	0.32
PLK1(42)	0.90	0.20	0.02	0.90	0.00	0.00	PKA alpha(31)	0.94	0.92	0.39	0.92	0.83	0.15
GRK_group(37)	0.91	0.67	0.05	0.89	0.00	0.00	IKK_group(35)	0.89	0.27	0.11	0.91	0.00	0.00
EGFR(61)	0.92	0.66	0.34	0.88	0.00	0.00	CaM-KIIalpha(34)	0.92	0.63	0.18	0.90	0.00	0.00
MAPK14(50)	0.92	0.57	0.50	0.90	0.22	0.04	GSK-3beta(52)	0.91	0.63	0.10	0.90	0.20	0.02
InsR(45)	0.92	0.60	0.36	0.83	0.60	0.07	CaM-KII_group(55)	0.92	0.63	0.18	0.92	0.89	0.15
CK2_group(248)	0.94	0.75	0.56	0.94	0.83	0.40	PKB_group(84)	0.94	0.87	0.46	0.95	0.87	0.57
AMPK_group(38)	0.93	0.86	0.32	0.91	1.00	0.06	CDK1(147)	0.94	0.63	0.84	0.92	0.65	0.28
MAPKAPK2(34)	0.92	0.62	0.24	0.90	0.00	0.00	CDK2(78)	0.93	0.61	0.78	0.91	0.45	0.07
CK1_group(33)	0.91	0.50	0.12	0.91	0.00	0.00	CK2 alpha(127)	0.94	0.77	0.52	0.93	0.73	0.32
PKA_group(330)	0.95	0.83	0.56	0.96	0.90	0.58	Lyn(48)	0.93	0.81	0.27	0.88	0.00	0.00
PKC alpha(188)	0.93	0.75	0.27	0.92	0.78	0.11	RSK_group(23)	0.95	0.81	0.57	No data
Syk(51)	0.94	0.75	0.53	0.86	0.30	0.07	DNA-PK(21)	0.93	0.60	0.57
Fyn(49)	0.91	0.42	0.10	0.90	0.00	0.00	Aurora(55)	0.93	0.81	0.31
MAPK_group(52)	0.93	0.62	0.50	0.93	1.00	0.22	Met(26)	0.95	0.69	0.85
MAPK3(88)	0.94	0.68	0.69	0.95	0.88	0.55	PHK_group(21)	0.92	0.67	0.29
MAPK1(117)	0.95	0.67	0.76	0.93	0.67	0.42	GRK-2(29)	0.92	1.00	0.10
MAPK8(36)	0.93	0.59	0.61	0.90	0.00	0.00	ROCK_group(23)	0.92	0.67	0.26
Lck(54)	0.93	0.94	0.30	0.90	0.00	0.00	FGFR1(23)	0.90	0.42	0.22
PKC_group(236)	0.93	0.76	0.26	0.93	0.85	0.24	PDGFR(21)	0.94	0.83	0.48
Src(154)	0.92	0.61	0.24	0.90	0.05	0.01	CK1(39)	0.92	0.62	0.21
IGF1R(31)	0.92	0.69	0.58	0.84	0.50	0.09	CDK5(22)	0.95	0.76	0.59
ATM(57)	0.95	0.85	0.60	0.97	0.91	0.75	PAK1(28)	0.91	0.60	0.11

ACC, P, and R indicate accuracy, precision, and recall, respectively. The mean accuracy, precision, and recall of the new method for 36 kinases are 0.93, 0.67, and 0.40, respectively while those of AutoMotif are 0.91, 0.47, and 0.17, respectively. The values in brackets represent number of known phosphorylation sites in the reference set. Kinase groups which show better performance in our method compared to AutoMotif are bolded.

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