Figure 3

Progression through the analysis process increases consistency of average cluster profiles. Step 1 of the analysis process was performed on each experiment individually and the average profile for each cluster was plotted. The resulting data sets were analyzed with the FOM and clustered using k-means into 12 clusters. Experiment 1 (A) portrays the DC maturation process as mostly up-regulated (orange profiles), whereas experiment 2 (B) portrays it as mostly down-regulated (blue profiles). Next, Steps 1 and 2 were performed on experiments 1 (C) and 2 (D). The resulting data sets from each experiment were analyzed with the FOM and clustered using k-means into 8 clusters. These clusters are now more consistent across experiments, however, experiment 2 (D) is now showing DC maturation to be more up-regulated than experiment 1 (C). Finally, Step 3, consensus clustering, was performed on experiments 1 (E) and 2 (F) using the parameters defined in Methods. These clusters are now consistent across experiments. The 1 hour time point was not used for filtering or clustering, and is shown for reporting purposes only.