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ReadMe.txt
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ReadMe.txt
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Matlab code for the calculation of the transcription factor activities (folder 1) and correlation (folder 2).
Software : Matlab 2018b
1_Network Component Analysis
- Run A_Network_Component_Analysis.m
- Load SupplementaryTables.xlsx
*********************Information****************************
A_Network_Component_Analysis.m - calculates the transcription factor activites in 100 runs with randomized starting points
B_bootstrapping_NCA_95CI.m - calculates the average transcription factor activity and the 95% - confidence intervals (CI)
Input:
Connectivity matrix and log10 - gene expression data imported from the supplementary tables.
Output:
NCA_struct_log10.mat - log10 - transcription factor activities, connectivity strength, squared 2-norm of the residual, the residual, and the final average deviation from the real gene expression data (accuracy) for each of the 100 iterations
NCA_result_log10.mat - average log10 - transcription factor activities ('P_mean') of the 100 randomized calculations and the 95%-CI ('P_up' & 'P_lo')
Note:
With randomized starting points for each of the 100 calculations, final average transcription factor activities can slightly differ from the final results from the Supplementary Tables.
2_Kinetic Correlation
- Run Kinetic_Correlation.m
- Load SupplementaryTables.xlsx
*********************Information****************************
Kinetic_Correlation.m - calculates the correlation coefficient of a activatory or inhibitory kinetic between the transcription factor activity and the metabolite level
Input:
Relative metabolite abundances and and log10 - transcription factor activities imported from the supplementary tables.
Output:
corr_result.mat - correlation coefficients for the kinetic fit
RSQ0 - without a shift between transcription factor activity and metabolit level
RSQ1 - with a shift of -1 between transcription factor activity and metabolite level
RSQ - best correlation coefficient between transcription factor activity and metabolite level
LAG - the corresponding time shift for correlation coefficient