Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins

Table 4 Comparison of the Sig and Sig' scoring for the top ranking motifs matching the known interaction motif.

Dataset^a	Sig'^b	Sig^c	ELM^d	Motif^e	k (N)^f
LIG_CtBP	3.4E-13	2.5E-09	P. [DEN]L [VAST]	P [ILM]DL (1)	15(30)
TRG_ER_KDEL_1	1.9E-11	3.0E-15	[KRHQSAP] [DENQT]EL$	DE.$ (1)	9(11)
LIG_PCNA	2.2E-11	1.7E-09	Q.. [ILM].. [FHM] [FHM]	Q.. [IL]..FF (1)	11(19)
MOD_SUMO	5.2E-11	1.1E-05	[VILAFP]K. [EDNGP]	V.VK.EP (1)	4(29)
LIG_SH3_2	6.7E-05	5.1E-04	P..P. [KR]	P. [LV]P. [KR] (1)	5(7)
LIG_AP_GAE_1	1.9E-04	4.0E-03	[DE] [DES].F. [DE] [LVIMFD]	D.F..F.S..P (1)	3(7)
LIG_Dynein_DLC8_1	6.0E-04	7.0E-03	[KR].TQT	K.TQ.P (1)	3(7)
LIG_RGD	9.6E-04	5.0E-03	RGD	RGD (1)	6(13)
LIG_CYCLIN_1	2.0E-03	0.012	[RK].L.{0,1} [FYLIVMP]	RR.L.{0,1}F (1)	4(18)
LIG_Clathr_ClatBox_1	0.011	0.054	L [ILM]. [ILMF] [DE]	[FL].D [FLM] (1)	8(14)
LIG_14-3-3_1	0.013	0.186	R. [^P] [ST] [^P]P	R.R..S (1)	4(4)
LIG_NRBOX	0.014	0.082	L..LL	L..LL. [ST] (2)	5(8)
LIG_RB	0.96	1.00	[LI].C. [DE]	E.L.C.E (29)	3(25)
LIG_14-3-3_3	0.95	1.00	[RHK] [STALV]. [ST]. [PESRDIF]	R [ST].S (13)	7(7)
LIG_HP1_1			P.V. [LM]		0(8)
MOD_N-GLC			N [^P] [ST]		0(5)
TRG_LysEnd_APsAcLL_1			[DER]...L [LVI]		0(10)

(a) The ELM dataset used. (b) The Sig' score of the top ranking motif matching the known interaction motif. (c) The Sig score of the top ranking motif matching the known interaction motif. (d) The regular expression of the true functional motif. (e) The regular expression of the top ranking motif that matches the known ELM. Significant motifs (p < 0.01) are shown in bold. (f) The number of proteins in the dataset containing the variant of the motif discovered and the number of proteins in the dataset (in brackets)

ISSN: 1471-2105