Autoantibodies and cytokine levels stratified according to RF seropositivity. Autoantibody and cytokine levels are higher in rheumatoid factor (RF)-positive RA than in RF-negative RA. Serum samples from 78 patients with RF-positive RA and from 42 patients with RF-negative RA were analyzed. 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.