Figure 1.

Unsupervised clustering of gene expression from patients with OA. RNA-Seq data from 44 PLC cartilage samples taken at total knee replacement and 10 non-OA PLC samples were normalised and batch effect corrected. Principal component analysis of the data was performed and the first and second (PC1 and PC2) principal components are shown (A). Network-based NMF or standard NMF was used to cluster the patients with OA into subgroups with variable numbers of predefined clusters (k). Patient co-clustering matrices are coloured to show patient pairwise co-occurrence in the same cluster across the 500 clustering runs (B). Silhouette scores were used to assess the optimal number of clusters (C) and the patient fit to a subgroup (D). NMF, negative matrix factorisation; OA, osteoarthritis; PLC, posterior lateral condyle.