Hierarchical gene clustering in rheumatoid arthritis (RA) and control synovia at different stages of progression. Samples from four early RA (eRA) patients, four long-standing RA (LS RA) patients, and seven controls (C) were studied by microarray analysis. Transcripts were selected with a supervised statistical one-class t test with the adjusted Bonferroni correction (P < 0.01). Patients are indicated as vertical column headings, and gene symbols of transcripts are given in horizontal rows. Transcript levels are expressed as the ratio sample level/median control level. Scale bar (log2 ratio): low (green), high (red), or ratio of 1 (black) expression in the sample versus the median control value (gray squares are missing values). (a) Visualization of 719 transcripts able to distinguish LS RA from early RA patients. (b) Visualization of 116 transcripts able to distinguish early RA patients from controls. (c) Visualization of 52 transcripts able to distinguish LS RA patients from controls. Each clustering is divided in two, yielding clusters 1 and 2, indicated by vertical bars.