Predicting direct protein interactions from affinity purification mass spectrometry data

Table 2 Performance of quasi-clique predictions

Network	k= 7				k= 6				k= 5
	real	pred.	FD(%)	FN(%)	real	pred.	FD(%)	FN(%)	real	pred.	FD(%)	FN(%)
Yu	42	54	22.22	0	66	104	36.53	0	146	308	55.19	5.48
DIP	0	42	100	0	86	112	26.79	4.65	184	266	35.34	6.52
PAM	0	31	100	0	0	45	100	0	0	96	100	0
DM	254	346	28.32	2.36	194	267	29.21	2.57	488	718	34.96	4.30

Number of edges that belong to maximal cliques of size k. Real: actual number of edges that belong to maximal cliques of size k; pred: predicted number of maximal k-clique edges; FD(false discovery ratio): percentage of false-positives in the predicted set; FN(false negative ratio): percentage of false-negatives in the real set.

ISSN: 1748-7188