As a first step, characteristics of the data were summarized in a number of well-chosen features: slopes between adjacent time points, maximum and minimum expression ratios, time of maximum and minimum expression, and steepest positive and negative slope, for a total of 12 features.
Carrying out a similar analysis on the sets of down-regulated genes (using the minimum expression value over time-points 0 4 h in all six agents) did not yield any significant results.
Further, genes with the highest transformed intensity smaller than two times the minimum expression across all samples of each dataset were deleted.
A time point with the minimum expression level of the regulator gene becomes a splitting point of the time span.
The times when maximum and minimum expression were observed by microarray.
Therefore, only genes with a minimum expression change of log2 fc ≥ 0.75 during time-course were considered.
The differences between maximum, or minimum, expression and the respective rate values were calculated to determine the time to maximum or minimum expression.
Lastly, we determined the time, or number of stages, to maximum or minimum expression by subtracting the maximum or minimum expression value for each regulated gene from the corresponding rate value.
We set the minimum expression TPM cutoff to 0.01.
Table 2C, D, and E list up-regulated and down-regulated genes and genes with alternated up- and down-regulations, respectively.> -wrap-foot> 2A: genes with a statistically significant differential expression at minimum one time point after LPS-induction.
