Figure 2: Exploring performance of NBS through simulation.
(a) TCGA somatic mutations for ovarian cancer (top left) are combined with the STRING human protein interaction network (bottom left) to generate simulated mutation data sets embedded with known network structure (right). (b) Accuracy with which NBS clusters recover simulated subtype assignments, evaluated with and without network smoothing and using non-negative matrix factorization (NMF) versus hierarchical clustering. Accuracy is calculated as the Adjusted Rand Index57 of overlap between the clusters and correct subtype assignments, for which a score of 0 represents random overlap and 1 represents perfect overlap. Simulation was performed with a driver mutation frequency f = 7.5% with a single network module assigned to each subtype. (c) Accuracy landscape of NBS across varying driver mutation frequency and module size. (d) As in c, for a standard non-network–based clustering approach. (e) As in c, using a permuted network.
