Workflow of experiments and types of analysis. Upper panel: in the discovery steps, synovial antigen microarrays and multiplex cytokine assays were employed to determine candidate molecules that are differentially expressed in pretreatment sera of etanercept responders (≥ ACR50) and nonresponders (< ACR20). Multiple array experiments were performed, each followed by significance analysis of microarrays (SAM) to identify the highest-scoring discriminators. Middle panel: further testing was performed with three independent cohorts using standard ELISAs, followed by prediction of response in three cohorts of etanercept-treated patients using prediction analysis of microarrays (PAM). Bottom panel: for training and testing, PAM was used to identify the best discriminators (training step; which identified a 24-biomarker panel) and then the utility of these discriminators for predicting response to etanercept was determined (testing). ACR, American College of Rheumatology response.