Top OA cytoscape clusters identify key model components.

(A) Affymetrix microarray data from 50 knee OA patients were collected from the Gene Expression Omnibus database, normalised, and the differentially expressed genes combined. ARACNE then inferred the interactions between these genes providing mutual information (MI) values that could be visualised using Cytoscape. The nodes (blue dots) represent differentially expressed genes and the edges are the MI values. Using clusterMaker these genes were then clustered based on MI values. The 14 largest clusters are represented here as they showed significant enrichment during DAVID analysis. (B) Overlaying the model genes to this clustered network highlighted the genes that were present. Genes shown to be present (dark blue) are SMAD1, TGFBR1 (Alk5), FOS (cFos) and JUNB. These were extracted along with all the genes that directly interacted with them (blue), to create the sub-networks shown.