Table 3.

The contents of each folder produced by Steps 2–7 of the Pipeline for Dynamic Gene Expression Data

File name	Description
Step 2
raw_data.mat	A Matlab file containing the raw unprocessed data (if .cell files are available)
processed_data.mat	A Matlab file containing the processed data (if .cell files are available)
Step 3
Matlab_Workspace3.mat	A Matlab file containing all the variables that the pipeline has required thus far.
Derivative_Fitted_Curves.csv	The first derivative of the estimated smooth trajectories of each gene expression over time.
DRG.csv	The probe set ids and the time course genes expression of each of the Dynamic Response Genes.
F_value.csv	The F-value for each gene.
Fitted_curves.csv	The estimated smooth trajectories of each gene expression over time.
Index_Ftest_DRGs.csv	The index of the DRGs ranked by their F-Statistic.
Index_Ftest.csv	The index of the probe set ids ranked by their F-Statistic.
Probe_set_ID_Ftest_DRG.csv	The probe set ids of the DRGs ranked by their F-Statistic.
Step 4
Matlab_Workspace4.mat	A Matlab file containing all the variables that the pipeline has required thus far.
Cluster_IDX.csv	The cluster index for each of the DRGs.
Cluster_MT.csv	The probe set ids for each of the DRGs and a number indicating which type of module this probe set belongs to SGM (1), SSM (2), MSM (3) and LSM (4).
GRMs.pdf	A file containing a plot of the time-course patterns for all the genes in each GRM.
Step 5
Matlab_Workspace5.mat	A Matlab file containing all the variables that the pipeline has required thus far.
M1/Chart_report_of_M1.csv	The annotation and enrichment analysis which highlights the most relevant terms associated with the genes contained in GRM 1. There is a folder and file for each GRM.
M1/Table_report_of_M1.csv	The annotation and enrichment analysis which highlights the most relevant terms associated with the genes contained in GRM 1. There is a folder and file for each GRM.
Step 6
Matlab_Workspace6.mat	A Matlab file containing all the variables that the pipeline has required thus far.
Coefficients.xls	The estimated regulation effects ${\left\{{\hat{\beta }}_{p,q,j}\right\}}_{p=0}^Q$
Dependency_matrix.xls	The GRMs inward and outward connections.
Step 7
Matlab_Workspace7.mat	A Matlab file containing all the variables that the pipeline has required thus far.
Adjacency_matrix.xls	The estimated regulation effects ${\left\{{\hat{\alpha }}_{p,q,j}\right\}}_{p=1}^Q$
Dependency_matrix.xls	The GRMs inward and outward connections.
Network_Statistics.xls	The Network metrics for the GRN.
Node_metrics.xls	The Network metrics for the GRMs.
Network_plot.pdf	A plot of the GRNs.