Figure 1.

Longitudinal study design and gene filtering results. Blood was sampled from eight patients at five different time points: before the start of GA treatment as well as after one day, one week, one month and two months. The expression of 18,862 genes was measured in monocytes with Affymetrix microarrays, and transcript levels during therapy were compared to the pre-treatment levels. t-test P-values and MAID-scores were used to determine differentially expressed genes. For instance, when comparing the baseline levels with the expression levels after one day, 438 genes survived the MAID analysis criterion (|MAID-score| > 2) and 1,124 genes survived the paired t-test criterion (P-value < 0.05). In combination, this resulted in 171 filtered genes: 101 were up-regulated (red arrow) and 70 were down-regulated (green arrow). For each time point comparison, a similar number of genes were filtered. However, the overlap of these four gene lists was relatively small (n = 45). When taken together, 463 different genes were identified to be differentially expressed within the first two months of GA therapy.