Evaluation of clustering algorithms for protein-protein interaction networks

BMC Bioinformatics

Table 4 Schematic illustration of a contingency table, and the derived statistics

Counts
T	cluster 1	cluster 2	cluster 3	cluster 4	cluster 5	sum	complex size
complex 1	7	0	0	0	0	7	7
complex 2	0	6	8	0	0	14	14
complex 3	0	0	0	14	3	17	20
complex 4	0	0	0	4	5	9	8
sum	7	6	8	18	8	47
cluster size	7	6	8	16	8
Positive Predictive Value (PPV)
PPV	cluster 1	cluster 2	cluster 3	cluster 4	cluster 5
complex 1	1	0	0	0	0
complex 2	0	1	1	0	0
complex 3	0	0	0	0.78	0.38
complex 4	0	0	0	0.22	0.62
cluster-wise PPV	1	1	1	0.78	0.62
Sensitivity
Sn	cluster 1	cluster 2	cluster 3	cluster 4	cluster 5	complex-wise Sn
complex 1	1	0	0	0	0	1
complex 2	0	0.43	0.57	0	0	0.57
complex 3	0	0	0	0.70	0.15	0.70
complex 4	0	0	0	0.50	0.62	0.62
Frequency per row
F _row	cluster 1	cluster 2	cluster 3	cluster 4	cluster 5
complex 1	1	0	0	0	0
complex 2	0	0.43	0.57	0	0
complex 3	0	0	0	0.82	0.18
complex 4	0	0	0	0.44	0.56
Separation
C	cluster 1	cluster 2	cluster 3	cluster 4	cluster 5	complex-wise separation
complex 1	1	0	0	0	0	1
complex 2	0	0.43	0.57	0	0	1
complex 3	0	0	0	0.64	0.07	0.71
complex 4	0	0	0	0.10	0.35	0.45
cluster-wise separation	1	0.43	0.57	0.74	0.41

ISSN: 1471-2105