Autoantibodies and cytokine levels stratified according to anti-CCP seropositivity. Autoantibody and cytokine levels are higher in anti- cyclic citrullinated peptide (CCP)-antibody-positive than in anti-CCP-antibody-negative RA. Serum samples from 73 patients with anti-CCP-antibody-positive RA and from 47 patients with anti-CCP-antibody-negative RA were analyzed. Chips containing CCP were excluded from this analysis. Autoantibody reactivity was assessed on the IMPACT platform and cytokine levels were measured in a bead-based assay run on the Luminex platform. For assays run on the IMPACT platform, values were normalized as described in the methods. Significance Analysis of Microarrays (SAM) followed by a hierarchical clustering algorithm were used to determine cluster relations that group patient samples (top dendrogram) and antigen reactivities (right dendrogram) on the basis of similarities in patient autoantibody and cytokine profiles (false discovery rate < 1). Dendrogram branch lengths and distances between nodes illustrate the extent of similarities in antigen reactivity and cytokine levels, with blue representing a decrease relative to the mean value obtained in samples from healthy individuals, yellow no change, and red an increase. Cit, citrullinated; COMP, cartilage oligomeric matrix protein; FGF-2, fibroblast growth factor 2; GM-CSF, granulocyte macrophage colony-stimulating factor; IL, interleukin; RF, rheumatoid factor; TNFα, tumor necrosis factor α.