BMC Genomics

Table 3 Prediction results when combining module-based CCS, orthology relationships, and neighboring proteins.

From: Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

		0.3			0.5			0.7
	# terms	P	R_pp	# terms	P	R_pp	# terms	P	R_pp
dme	6242	0.50	0.29	5072	0.52	0.25	1522	0.73	0.32
sce	3567	0.61	0.27	2581	0.71	0.28	1303	0.83	0.40
rno	1125	0.63	0.20	485	0.67	0.27	1185	0.85	0.30
hsa	1489	0.56	0.29	368	0.85	0.34	223	0.89	0.34
sce	1870	0.60	0.25	1206	0.61	0.17	229	0.86	0.24
hsa	13975	0.46	0.35	4418	0.57	0.36	723	0.73	0.33
dme	18638	0.62	0.41	16225	0.61	0.38	3462	0.71	0.48
sce	16544	0.72	0.44	15524	0.72	0.43	4135	0.84	0.55
hsa	3314	0.47	0.25	439	0.75	0.28	160	0.91	0.41
dme	5190	0.58	0.22	4586	0.59	0.23	866	0.81	0.29
cel	2464	0.47	0.27	1796	0.56	0.27	256	0.65	0.31
sce	5361	0.70	0.31	5126	0.71	0.32	1212	0.80	0.37
mmu	1212	0.66	0.17	459	0.81	0.32	53	0.81	0.34
hsa	3301	0.48	0.28	1658	0.57	0.33	436	0.65	0.81
dme	5561	0.56	0.29	4642	0.57	0.29	1400	0.59	0.55
sce	5159	0.63	0.31	4906	0.63	0.31	2140	0.73	0.72
average	5870	0.58	0.29	4343	0.65	0.30	1160	0.77	0.42

Precision (P) and per-protein recall (Rpp) are estimated for low (0.3), medium (0.5) and high (0.7) functional similarity/conservation thresholds.

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