Data:subset_development_4t_data.zip
Covariates:development_covariates.txt

Variability associated to each factor:

• Time 25.86 %
• Treatment+TimexTreatment 37.52 %
• Residuals 36.62 %

Variability explained for each submodel :

• With 2 components, Submodel Time explains 93.66% of variation of factor Time. (Component 1: 49.66% and Component 2: 44%).
• With 2 components, Submodel Treatment+TimexTreatment explains 71.86% of variation of factor Treatment+TimexTreatment.(Component 1: 44.18% and Component 2: 27.67%).

By applying ASCA-Functional to the first component of the submodel Treatment+TimexTreatment and considering a significant level of 0.05 in the GSA analysis we detected as significant 13 functional categories. The categories with an adjusted p-value less than 0.05 appear in the first two tables of the ASCA-Functional results.

General trends showed with ASCA-genes module suggest that a quadratic model can be adequate to study gene expression evolution. By applying maSigPro with degree=2 (the quadratic model), R-squared=0.8 and alpha=0.05 we obtained as significant:

• 1307 genes with changes in the trajectory of A.
• 1158 genes with differences between the trajectories of the groups B and A.
• 1282 genes with differences between the trajectories of the groups C and A.

We represent in 9 groups the trajectories of the second gene-selection (1158 genes).

By applying maSigFun with degree=2, R-squared=0.4, alpha=0.05 and annotations GO biological process of Human organism we selected as significant the following categories:

• GO:0006842 tricarboxylic acid transport
• GO:0010544 negative regulation of platelet activation
• GO:0015746 citrate transport

The trajectory plots of these categories are the following:

Finally we run PCA-maSigFun with degree=2, R-squared=0.8 and alpha=0.05. This tool selected as statistically significant the following number of categories for the experimental groups:

• 1466 categories with changes in the trajectory of A.
• 1100 categories with differences between the trajectories of the groups B and A.
• 1469 categories with differences between the trajectories of the groups C and A.