Discovering multiple realistic TFBS motifs based on a generalized model

Chan, Tak-Ming; Li, Gang; Leung, Kwong-Sak; Lee, Kin-Hong

doi:10.1186/1471-2105-10-321

BMC Bioinformatics

Table 5 Experiments on the 8 real datasets (1).

From: Discovering multiple realistic TFBS motifs based on a generalized model

Datasets	GALF-G			GAME
	sPPV	sSn	sF	sPPV	sSn	sF
CREB
R ₁	0.76 ± 0.00	0.68 ± 0.00	0.72 ± 0.00	0.34 ± 0.37	0.35 ± 0.36	0.34 ± 0.36
R ₂	0.75 ± 0.06	0.68 ± 0.04	0.71 ± 0.05	0.33 ± 0.34	0.34 ± 0.35	0.33 ± 0.34
R ₃	0.76 ± 0.00	0.68 ± 0.00	0.72 ± 0.00	0.39 ± 0.36	0.38 ± 0.35	0.38 ± 0.35
CRP
R ₁	0.94 ± 0.00	0.73 ± 0.02	0.82 ± 0.01	0.79 ± 0.02	0.78 ± 0.00	0.78 ± 0.01
R ₂	0.89 ± 0.02	0.74 ± 0.00	0.81 ± 0.01	0.82 ± 0.00	0.78 ± 0.00	0.80 ± 0.00
R ₃	0.79 ± 0.06	0.71 ± 0.04	0.75 ± 0.05	0.93 ± 0.03	0.66 ± 0.03	0.77 ± 0.01
ERE
R ₁	0.64 ± 0.02	0.83 ± 0.02	0.72 ± 0.02	0.53 ± 0.00	0.80 ± 0.00	0.63 ± 0.00
R ₂	0.67 ± 0.03	0.85 ± 0.03	0.75 ± 0.03	0.55 ± 0.04	0.79 ± 0.02	0.65 ± 0.02
R ₃	0.77 ± 0.05	0.84 ± 0.01	0.80 ± 0.03	0.60 ± 0.04	0.80 ± 0.03	0.69 ± 0.03
E2F
R ₁	0.79 ± 0.02	0.84 ± 0.03	0.81 ± 0.02	0.76 ± 0.09	0.84 ± 0.10	0.80 ± 0.10
R ₂	0.79 ± 0.00	0.81 ± 0.00	0.80 ± 0.00	0.72 ± 0.00	0.85 ± 0.00	0.78 ± 0.00
R ₃	0.79 ± 0.00	0.81 ± 0.00	0.80 ± 0.00	0.75 ± 0.00	0.78 ± 0.00	0.76 ± 0.00
MEF2
R ₁	0.93 ± 0.00	0.82 ± 0.00	0.88 ± 0.00	0.65 ± 0.29	0.75 ± 0.33	0.69 ± 0.30
R ₂	0.94 ± 0.00	1.00 ± 0.00	0.97 ± 0.00	0.73 ± 0.26	0.77 ± 0.28	0.75 ± 0.27
R ₃	1.00 ± 0.00	1.00 ± 0.00	1.00 ± 0.00	0.93 ± 0.00	0.83 ± 0.03	0.88 ± 0.01
MyoD
R ₁	0.33 ± 0.04	0.42 ± 0.05	0.37 ± 0.04	0.13 ± 0.10	0.16 ± 0.10	0.14 ± 0.10
R ₂	0.21 ± 0.01	0.23 ± 0.02	0.21 ± 0.05	0.12 ± 0.11	0.16 ± 0.16	0.11 ± 0.11
R ₃	0.25 ± 0.00	0.29 ± 0.00	0.25 ± 0.06	0.13 ± 0.12	0.14 ± 0.15	0.13 ± 0.14
SRF
R ₁	0.72 ± 0.04	0.87 ± 0.03	0.79 ± 0.03	0.71 ± 0.02	0.87 ± 0.04	0.78 ± 0.03
R ₂	0.74 ± 0.03	0.78 ± 0.04	0.76 ± 0.03	0.66 ± 0.02	0.87 ± 0.01	0.75 ± 0.02
R ₃	0.70 ± 0.02	0.74 ± 0.08	0.72 ± 0.05	0.70 ± 0.06	0.77 ± 0.05	0.73 ± 0.02
TBP
R ₁	0.86 ± 0.01	0.82 ± 0.02	0.84 ± 0.01	0.80 ± 0.08	0.75 ± 0.12	0.77 ± 0.09
R ₂	0.87 ± 0.02	0.86 ± 0.02	0.87 ± 0.01	0.79 ± 0.05	0.78 ± 0.04	0.78 ± 0.03
R ₃	0.87 ± 0.02	0.86 ± 0.02	0.86 ± 0.02	0.71 ± 0.17	0.74 ± 0.18	0.72 ± 0.18
Average	0.74	0.75	0.74	0.61	0.66	0.62

Average results (precision (sPPV), recall (sSn) and F-scores (sF) are averaged separately) of GALF-G and GAME on the 8 datasets. Each range R_i= [w + (i - 1) - 3, w + (i - 1) + 3] in general indicates different shifts i from the true width w. ± shows the standard deviation (based on 20 independent runs of each dataset with each range). The results with best sF among this table and Table 6 are shown in bold.

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ISSN: 1471-2105

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