Both the maximum and the minimum expression ratios per gene were determined from these 12 ratios (i.e. sample size).
The maximum and minimum expression ratios were important for finding genes with the same magnitude of expression.
Biologically, maximum and minimum expression ratios reflected the impact of signaling via specific transduction pathways and represented the best window of measurement of this change [ 56].
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.
Genes identified to be differentially expressed had a minimum 2-fold expression ratio at any time point.
For each expression data set, only genes that were detected as expressed were taken into consideration when calculating the correlation between the male/female expression ratio and minimum DCC distance.
Briefly this involved calculating the MFC (maximal fold change), i.e. the ratio of the maximum and minimum expression values for all microarrays performed in the experiment, and the CV, i.e. the coefficient of variation.
For each family of TF (F1, F2, ‥, Fk) and each tissue T, we computed the ratio RI = (Emax-Emax2)/(Emax-Emin), where Emax and Emin represent the maximum and the minimum expression levels and Emax2 represents the second highest expression among the family members in tissue T. The ratio RI captures the increase in expression, i.e., high value of RG represents an expression increase.
In order to test this hypothesis, for each family with k TFs (TF1, TF2, ‥, TFk) and each tissue T, we computed the ratio R = (Emax-Esim)/(Emax-Emin), where Emax and Emin represent the maximum and the minimum expression levels, respectively, among the family members in tissue T. Thus, the R value is normalized for family-specific and tissue-specific gene expression.
Two criteria were used to generate a list of significantly and consistently altered genes: a) genes consistently expressed (Student's t-test, p ≤ 0.1) and substantially altered at a mean absolute log2 expression ratio of at least 0.585 (50% increase or decrease in expression); and b) genes consistently altered by a minimum absolute log2 expression ratio of 0.585 in all three replicates.
