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For this reason we have developed the WDM, where the state of each element of the network is represented by its average expression over a time window.
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The relative expression of each gene was calculated by dividing its expression level by the average expression of the 3 reference genes for each sample.
Expression for each probe was normalized by GC-RMA, and using the most highly expressed probe set for each gene of interest, the relative expression of each gene was calculated by dividing its expression level by the average expression of the 3 reference genes for each sample.
Hence it is appropriate to express each principal component by the average expression of a (small) group of proteins in order to benefit from the intrinsic noise suppression of averaging as well.
Relative expression levels were normalized by the average expression level of Actb and Sdha and are expressed as relative values with respect to the expression level in the control condition.
Only miRNA target seeds from the top 100 expressed miRNAs by average expression level across the samples were used in the target prediction.
The expression levels of a gene expressed in different expression libraries were estimated by calculating average expression values in all libraries considered (Supplementary Tables S2 and S3 contain library information).
For CD4, we divided the non-Treg CD4+ T cells by their average expression of a predefined cytotoxic signature (PRF1, NKG7, GZMK, GZMA and CST7) into three groups (low, medium and high) and compared the high to the low groups.
The clusters are summarized by the average expression profiles, per cluster, that is plotted against time (See Figure 2).
Fold changes were calculated from the average expression for each line divided by the average expression in all controls used in the same experiment.
This timeline is confirmed by the data presented, implicating that most expression profiles return to baseline at 56 days, as shown by the average expression profiles (Figure 3).
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