Stratification of rheumatoid arthritis (RA) transcriptional heterogeneity into homogeneous molecular phenotypes. (A) Two-dimensional hierarchical clustering of approximately 7,000 probes (rows), representing quantile-normalized and scaled expression values of the top 40% most variable probe sets (variability assessed using SD), in 49 RA patients (columns) inferring five molecular subgroups of synovial tissues. Patient-sample ordering and dendrogram based on agglomerative hierarchical clustering (Ward method): resulting tree used to select patient subgroups; number of patient subgroups selected to maximize mean silhouette width and k-nearest neighbor distances (k = 5 considered optimal). z-score-based color intensity scale for each probe in each sample is shown. Patient samples clustering into five main branches are color-coded left to right (bottom of the heatmap): C1 = red (n = 8), C2 = purple (n = 14), C3 = gray (n = 16), C4 = green (n = 8), C5 = light blue (n = 3). (B) Heatmap depicting over-represented Database for Annotation, Visualization and Integrated Discovery biological process categories for genes upregulated in the four largest synovial clusters. Each column represents one cluster (C1 to C4), color-coordinated as in panel A. Each row corresponds to a biological process category. Heatmap colors reflect log10 (adjusted P-value) from modified Fisher exact test for categorical over-representation. Annotation for each cluster based on the key biological processes is indicated. BMP, bone morphogenetic protein; TGF, transforming growth factor; SMAD, Sma Mothers Against Decapentaplegic; NOD, nucleotide-binding oligomerization domain; JAK-STAT, Janus kinase-signal transducer and activator of transcription.