Improving protein function prediction methods with integrated literature data

BMC Bioinformatics

Table 4 Characterization of Annotations

	Source	Yeast MIPS	Yeast GO		Worm GO		Fly GO
			MF	BP	MF	BP	MF	BP
Annotation Terms		85	37	32	37	48	39	49
Percentage Unknown Nodes	PPI	23	38	28	41	51	39	42
	GENETIC	14	32	16	24	26	53	41
	COLIT	2	15	7	17	24	9	7
Percentage Connected to ≥ 1 Unknown	PPI	31	53	36	46	61	69	70
	GENETIC	14	40	24	53	50	32	17
	COLIT	4	34	18	53	59	33	28
Percentage Only Surrounded by Unknowns	PPI	4	9	5	17	29	15	16
	GENETIC	0.9	7	4	4	4	7	1
	COLIT	0.08	2	1	4	2	1	1
Percent Edges Connecting Nodes Sharing Function	PPI	37	18	36	10	6	10	14
	GENETIC	48	12	40	42	50	32	70
	COLIT	80	40	71	59	53	47	70

Various measures to characterize the completeness and connections among gold-standard annotations in the graphs. All values are given for all nodes in the Largest Connected Component of the graph. The number of nodes and edges from which these percentages are calculated are shown in panel 2 of Table 3. Unknown refers to proteins uncharacterized by the annotation source. Other abbreviations are as given in Table 3.

ISSN: 1471-2105