MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences

Wang, Dianhui; Tapan, Sarwar

doi:10.1186/1752-0509-6-S2-S4

BMC Systems Biology

Table 4 Sep(, ) score comparison among R, R_l, IC and MAP score

From: MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences

Result details: Sep(, ) ± E{std} on each dataset using 5000 random models
dg	TF	Sep (IC, R)	Sep (IC, R_l)	Sep (MAP, R)	Sep (MAP, R_l)	Sep (R, R_l)
	CREB	-0.099 ± 0.051	-0.080 ± 0.013	0.255 ± 0.030	0.268 ± 0.014	0.022 ± 0.047
	SRF	-0.104 ± 0.036	-0.133 ± 0.008	0.313 ± 0.020	0.294 ± 0.009	-0.022 ± 0.034
	TBP	-0.088 ± 0.025	0.056 ± 0.002	0.302 ± 0.014	0.395 ± 0.005	0.125 ± 0.020
	MEF2	-0.405 ± 0.088	0.092 ± 0.020	0.144 ± 0.049	0.446 ± 0.017	0.358 ± 0.041
dg ₁	MYOD	-0.113 ± 0.043	-0.022 ± 0.010	0.299 ± 0.025	0.356 ± 0.011	0.066 ± 0.037
	ERE	0.060 ± 0.027	0.057 ± 0.011	0.416 ± 0.017	0.414 ± 0.012	-0.008 ± 0.028
	E2F	-0.048 ± 0.032	0.064 ± 0.012	0.350 ± 0.018	0.419 ± 0.012	0.110 ± 0.027
	CRP	0.013 ± 0.032	0.070 ± 0.018	0.486 ± 0.018	0.516 ± 0.013	0.052 ± 0.028
	avg	-0.098 ± 0.042	0.013 ± 0.012	0.321 ± 0.024	0.388 ± 0.012	0.088 ± 0.033
	dm01g	-0.080 ± 0.042	0.024 ± 0.027	0.294 ± 0.024	0.361 ± 0.023	0.101 ± 0.035
	dm04m	-0.029 ± 0.038	0.026 ± 0.025	0.350 ± 0.022	0.384 ± 0.022	0.053 ± 0.033
	hm02r	-0.187 ± 0.067	0.089 ± 0.029	0.320 ± 0.037	0.478 ± 0.024	0.219 ± 0.043
	hm03r	-0.096 ± 0.045	0.076 ± 0.017	0.276 ± 0.026	0.389 ± 0.015	0.135 ± 0.037
	hm06g	-0.145 ± 0.068	0.001 ± 0.031	0.227 ± 0.040	0.325 ± 0.025	0.139 ± 0.051
	hm08m	-0.006 ± 0.048	0.082 ± 0.024	0.277 ± 0.030	0.340 ± 0.021	0.084 ± 0.041
	hm09g	-0.120 ± 0.087	-0.009 ± 0.041	0.211 ± 0.053	0.288 ± 0.035	0.114 ± 0.075
	hm10m	-0.070 ± 0.050	0.071 ± 0.027	0.290 ± 0.030	0.383 ± 0.022	0.134 ± 0.038
dg ₂	hm11g	-0.172 ± 0.062	0.077 ± 0.016	0.224 ± 0.036	0.388 ± 0.016	0.168 ± 0.045
	hm16g	-0.218 ± 0.100	0.000 ± 0.049	0.227 ± 0.056	0.364 ± 0.038	0.140 ± 0.077
	hm17g	-0.076 ± 0.052	-0.022 ± 0.026	0.379 ± 0.029	0.409 ± 0.021	0.065 ± 0.045
	hm20r	-0.344 ± 0.044	0.098 ± 0.002	0.234 ± 0.022	0.486 ± 0.006	0.322 ± 0.023
	hm21g	-0.183 ± 0.062	-0.075 ± 0.036	0.293 ± 0.035	0.357 ± 0.027	0.064 ± 0.051
	hm24m	-0.082 ± 0.052	0.024 ± 0.032	0.324 ± 0.031	0.390 ± 0.026	0.107 ± 0.042
	hm26m	-0.114 ± 0.067	0.177 ± 0.034	0.377 ± 0.039	0.540 ± 0.028	0.265 ± 0.044
	mus02r	-0.034 ± 0.110	-0.061 ± 0.058	0.409 ± 0.062	0.393 ± 0.046	0.004 ± 0.119
	mus10g	-0.630 ± 0.134	-0.052 ± 0.020	0.001 ± 0.076	0.355 ± 0.019	0.350 ± 0.056
	mus11m	-0.623 ± 0.098	-0.049 ± 0.021	0.050 ± 0.054	0.386 ± 0.019	0.340 ± 0.042
	yst08r	-0.019 ± 0.050	0.149 ± 0.024	0.037 ± 0.040	0.196 ± 0.019	0.131 ± 0.045
	yst09g	-0.253 ± 0.102	0.179 ± 0.036	-0.053 ± 0.073	0.310 ± 0.029	0.353 ± 0.056
	avg	-0.174 ± 0.069	0.040 ± 0.029	0.237 ± 0.041	0.376 ± 0.024	0.164 ± 0.050
	CREB	-0.102 ± 0.047	-0.056 ± 0.012	0.248 ± 0.028	0.280 ± 0.013	0.072 ± 0.042
	SRF	-0.085 ± 0.029	-0.131 ± 0.007	0.324 ± 0.016	0.296 ± 0.008	-0.026 ± 0.028
dg ₃	TBP	-0.080 ± 0.023	0.052 ± 0.002	0.307 ± 0.013	0.392 ± 0.005	0.129 ± 0.019
	MEF2	-0.420 ± 0.092	0.122 ± 0.020	0.132 ± 0.051	0.463 ± 0.017	0.372 ± 0.042
	MYOD	-0.115 ± 0.040	-0.017 ± 0.009	0.297 ± 0.023	0.358 ± 0.010	0.088 ± 0.034
	avg	-0.160 ± 0.046	-0.006 ± 0.010	0.262 ± 0.026	0.358 ± 0.011	0.127 ± 0.033
Result summary: E{Sep(, )} ± E{std} on each data group
	data group (dg)	Sep(IC, R)	Sep(IC, R_l)	Sep(MAP, R)	Sep(MAP, R_l)	Sep(R, R_l)
	dg ₁	-0.098 ± 0.042	0.013 ± 0.012	0.321 ± 0.024	0.388 ± 0.012	0.088 ± 0.033
	dg ₂	-0.174 ± 0.069	0.040 ± 0.029	0.237 ± 0.041	0.376 ± 0.024	0.164 ± 0.050
	dg ₃	-0.160 ± 0.046	-0.006 ± 0.010	0.262 ± 0.026	0.358 ± 0.011	0.127 ± 0.033
	avg	-0.144 ± 0.052	0.016 ± 0.017	0.273 ± 0.030	0.374 ± 0.015	0.126 ± 0.039

Remark: Sep(*, *) score is computed on a dataset using 5000 random set of k-mers generated from the dataset. It can be seen that the localized version improves MISCORE in terms of separability performance, i.e., Sep(R, R_l) > 0 holds for most of the cases. Sep(*, *) score comparison among other metrics show that MISCORE is likely to produce favorable separability performance than IC and MAP score.

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ISSN: 1752-0509

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