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 6 Experiments on the 8 real datasets (2).

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

Datasets	MEME			Weeder			FlexModule
	sPPV	sSn	sF	sPPV	sSn	sF	sPPV	sSn	sF
CREB					medium
R ₁	0.73	0.58	0.65	0.44	0.84	0.58	0.68 ± 0.04	0.76 ± 0.04	0.72 ± 0.04
R ₂	0.83	0.53	0.65	0.44	0.84	0.58	0.62 ± 0.22	0.69 ± 0.24	0.65 ± 0.23
R ₃	0.83	0.53	0.65	0.44	0.84	0.58	0.67 ± 0.07	0.72 ± 0.07	0.69 ± 0.07
CRP					large
R ₁	0.93	0.61	0.74	0.41	0.71	0.52	0.94 ± 0.14	0.55 ± 0.11	0.69 ± 0.12
R ₂	0.89	0.70	0.78	0.41	0.71	0.52	0.97 ± 0.07	0.56 ± 0.06	0.70 ± 0.06
R ₃	0.89	0.70	0.78	0.41	0.71	0.52	0.96 ± 0.13	0.50 ± 0.10	0.65 ± 0.11
ERE					large
R ₁	0.88	0.60	0.71	0.29	0.64	0.40	0.74 ± 0.03	0.85 ± 0.01	0.79 ± 0.02
R ₂	0.88	0.60	0.71	0.29	0.64	0.40	0.73 ± 0.02	0.85 ± 0.02	0.79 ± 0.02
R ₃	0.88	0.60	0.71	0.29	0.64	0.40	0.68 ± 0.17	0.77 ± 0.24	0.72 ± 0.21
E2F					large
R ₁	0.78	0.67	0.72	0.23	0.93	0.37	0.56 ± 0.28	0.58 ± 0.29	0.57 ± 0.28
R ₂	0.83	0.70	0.76	0.23	0.93	0.37	0.60 ± 0.29	0.60 ± 0.29	0.60 ± 0.29
R ₃	0.78	0.67	0.72	0.23	0.93	0.37	0.63 ± 0.25	0.62 ± 0.25	0.63 ± 0.25
MEF2					medium
R ₁	0.93	0.82	0.88	0.01	0.06	0.02	0.86 ± 0.02	1.00 ± 0.00	0.93 ± 0.01
R ₂	0.93	0.82	0.88	0.01	0.06	0.02	0.79 ± 0.27	0.90 ± 0.31	0.84 ± 0.29
R ₃	0.93	0.82	0.88	0.01	0.06	0.02	0.88 ± 0.02	0.99 ± 0.04	0.93 ± 0.02
MyoD					small
R ₁	0.00	0.00	0.00	0.07	0.10	0.08	0.00 ± 0.00	0.00 ± 0.00	0.00 ± 0.00
R ₂	0.00	0.00	0.00	0.07	0.10	0.08	0.00 ± 0.00	0.00 ± 0.00	0.00 ± 0.00
R ₃	0.00	0.00	0.00	0.07	0.10	0.08	0.00 ± 0.00	0.00 ± 0.00	0.00 ± 0.00
SRF					large
R ₁	0.65	0.86	0.74	0.54	0.63	0.58	0.64 ± 0.00	0.87 ± 0.02	0.73 ± 0.01
R ₂	0.70	0.86	0.78	0.54	0.63	0.58	0.63 ± 0.01	0.82 ± 0.05	0.71 ± 0.02
R ₃	0.70	0.86	0.78	0.54	0.63	0.58	0.64 ± 0.00	0.86 ± 0.01	0.74 ± 0.00
TBP					small
R ₁	0.70	0.67	0.69	0.56	0.90	0.69	0.47 ± 0.32	0.59 ± 0.40	0.53 ± 0.35
R ₂	0.70	0.67	0.69	0.56	0.90	0.69	0.41 ± 0.34	0.51 ± 0.42	0.45 ± 0.38
R ₃	0.70	0.67	0.69	0.56	0.90	0.69	0.45 ± 0.34	0.55 ± 0.41	0.49 ± 0.37
Average	0.71	0.61	0.65	0.32	0.60	0.40	0.61	0.63	0.61

Average results of MEME, Weeder and FlexModule in the same comparison experiments described in Table 5. Weeder was run with the width mode (small: 6, 8; medium: 6, 8, 10; large 6, 8, 10, 12) that are closest to the ranges R for each dataset.

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ISSN: 1471-2105

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