Research Paper Volume 5, Issue 1 pp 18—36

Figure 2. Age-associated alterations in NF-κB-dependent gene regulation in activated human peripheral blood CD4⁺ T lymphocytes. Total RNA was prepared from CD4⁺ T cells incubated at 37°C for 4h without further treatment, or treated with plate-bound anti-CD3 for 2h and 4h. Fluorescently labeled cRNA was hybridized to Illumina HumanRef-8 Expression BeadChip as described in the Methods Section. A, B, C left panels. Normalized hybridization data was analyzed using Parametric Analysis of Gene Set Enrichment (PAGE) (Broad Institute, M.I.T., Cambridge MA). Pathway Z-scores were averaged amongst less than 65 (Y), 50-64 (M), 65 and older (O) subjects. Pathways that were up-regulated after 2h or 4h of activation compared to untreated cells were first determined (Figure S4A). Thereafter, the top 20 pathways that continued to be up-regulated between 2h and 4h of activation were identified (y axis). The Z-score difference between 2h and 4h of activation is indicated in the x axis. Right panels ‘NF-κB induced’ pathway genes that were altered between 2h and 4h of activation are listed (y axis); Z-ratios for the difference in expression between 2h and 4h are shown on the x axis. Positive numbers indicate genes that are up-regulated between 2h and 4h; negative numbers denote genes that are down-regulated between 2h and 4h. Z-ratio values were greater than 1.5, p-values for all genes were <0.05.