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Source code for the article "Encoding growth factor identity in the temporal dynamics of a transcription factor under combinatorial regulation" by Sampattavanich et al.
MATLAB Python
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fig1B-EndoVSReporter
fig1C-S1G-WesternBlot
fig1D-2AB-SingleCellTraces
fig3-S2-fPCA
fig4-S3-S5AB-pulseScore-MI
fig5A-S4BD-mutation
fig5B-S4C-pharmInh
fig5C-MEKionF3aN400Pulsing
fig5D-TrendVsPulseScore
fig6B-DualSensor-BTCwithInh
fig6C-DualSensor-VaryingGF
fig6D-EKAREVPulsing
fig7-S7-BreastCancerCells
figS1BC-SegmentationAlgo
figS1E-pulsingVSiqr
rawdata/parentalVSReporter
.gitignore
LICENSE
README.md
summaryTable.docx

README.md

Sampattavanich et al., Cell Systems (2018)

Source code and example plots for the article "Encoding growth factor identity in the temporal dynamics of FoxO3 under combinatorial regulation by ERK and Akt" by Sampattavanich et al., Cell Systems (2018)

Each piece of source code is provided in a folder containing matlab or python scripts and all related functions. The main function to generate related figures are highlighted in bold.

To run this code, users must download related raw data from https://doi.org/10.6084/m9.figshare.c.4026994 and put these in the \rawdata folder placed at the top-most level of this git repository folder. users must also install functional data analysis MATLAB package from http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/Matlab/.

Figures Related files
Fig.1B Fig1B/createParentalVSReporter.m (Main script)
Rawdata/parentalVSReporter/*.* (download)
Fig.S1B and S1C FigS1BC/comparedataat15min.m (Main script)
Rawdata/parentalVSReporter/*.* (download)
Fig.1C and S1G Fig1C/fig1CS1G.m (Main script)
Rawdata/western/*.* (download)
Fig.S1E FigS1E/pulsing_vs_iqr.py (Main script)
Rawdata/Workspaces/130722_SCdyn.csv (download)
Rawdata/Workspaces/130722_Pav.csv (download)
Fig.1D and 2A&B Fig1D-2AB/fig1D.m (Main script)
Fig1D-2AB/fig2A.m (Main script)
Fig1D-2AB/fig2B.m (Main script)
Rawdata/Workspaces/site_x.mat for x = 4, 17, 37, 44, 57, 64(download)
Rawdata/Workspaces/harm_basis_130722_corrected_retracked_all_cleaned_late.mat (download)
Rawdata/Workspaces/fourier_signals_corrected_cleaned_newBTC2.mat (download)
Fig.3 and S2 Fig3-S2/fig3A.m (Main script)
Fig3-S2/fig3B.m (Main script)
Fig3-S2/fig3C.m (Main script)
Fig3-S2/fig3D.m (Main script)
Fig3-S2/figS2A.m (Main script)
Fig3-S2/figS2B.m (Main script)
Fig3-S2/figS2C.m (Main script)
Rawdata/Workspaces/site_x_130722_corrected_retracked_all_cleaned.mat for x = 17, 57, 64(download)
Rawdata/Workspaces/scores_early_5basis_noFGF_newBTC.mat (download)
Rawdata/Workspaces/harm_basis_fPCA_5basis_noFGF_newBTC_rot.mat (download)
Rawdata/Workspaces/harm_basis_50_to_600.mat (download)
Rawdata/Workspaces/harm_basis_130722_corrected_retracked_all_cleaned_late.mat (download)
Rawdata/Workspaces/site_4_130722_corrected_retracked_all_paper_cleaned.mat (download)
Rawdata/Workspaces/130722_SCfeat.csv (download)
Fig.4, S3 and S5A&B Fig4-S3-S5AB/fig4AB.m (Main script)
Fig4-S3-S5AB/fig4CDS3DS5AB.m (Main script)
Fig4-S3-S5AB/figS3A.m (Main script)
Fig4-S3-S5AB/figS3B.m (Main script)
Fig4-S3-S5AB/figS3C_lower.m (Main script)
Fig4-S3-S5AB/figS3C_upper.m (Main script)
Rawdata/Workspaces/ site_x_130722_corrected_retracked_all_cleaned.mat for x = 17, 57, 64(download)
Rawdata/Workspaces/harm_basis_fPCA_5basis_noFGF_newBTC_rot.mat (download)
Rawdata/Workspaces/ harm_basis_130722_corrected_retracked_all_cleaned_late_newBTC.mat (download)
Rawdata/Workspaces/scores_early_5basis_noFGF_newBTC.mat (download)
Rawdata/Workspaces/scores_early_5basis_noFGF_AKTi.mat (download)
Rawdata/Workspaces/scores_puls_corrected_retracked_all_cleaned_newBTC.mat (download)
Rawdata/Workspaces/scores_puls_corrected_retracked_all_cleaned_newBTC_ATKi.mat (download)
Fig.5A and S4B&D Fig5A-S4BD/fig5AS4BD.m (Main script)
Rawdata/Workspaces/site_x_04-15-2014_all_paper_cleaned.mat for x = 1,3,5,7,9,11,14,16,18,20,22,24,25,27,29,31,33,35,38,40,42,44,46,48,49,51,53,55,57,59 (download)
Rawdata/Workspaces/scores_04-15_new.mat (download)
Fig.5B and S4C Fig5B-S4C/fig5BS4C.m (Main script)
Rawdata/Workspaces/site_x_130722_corrected_retracked_all_paper_cleaned.mat for x = 1,2,4,37,39,40,41,42,44,61,62,64 (download)
Rawdata/Workspaces/scores_early_5basis_noFGF_AKTi.mat (download)
Rawdata/Workspaces/scores_early_5basis_noFGF_MEKi.mat (download)
Rawdata/Workspaces/scores_early_5basis_noFGF_newBTC.mat (download)
Rawdata/Workspaces/scores_puls_corrected_retracked_all_cleaned_newBTC.mat (download)
Rawdata/Workspaces/scores_puls_corrected_retracked_all_cleaned_newBTC_ATKi.mat (download)
Rawdata/Workspaces/scores_puls_corrected_retracked_all_cleaned_newBTC_MEKi.mat (download)
Fig.5C Fig5C /fig5C.m (Main script)
Rawdata/Workspaces/dists_04182014.mat (download)
Fig.5D Fig5D/fig5D.m (Main script)
Rawdata/Workspaces/c_signal_03302014.mat (download)
Rawdata/Workspaces/dists_04182014.mat (download)
Rawdata/Workspaces/scores_04182014.mat (download)
Fig.6B Fig6B/plot_exampleEKAREVvsF3aN400.m (Main script)
Fig6B/calculate_correlation.m (Main script)
Rawdata/dualsensors/*.* (download)
Fig.6C Fig6C/fig6C.m (Main script)
Rawdata/Workspaces/140215_SCdyn_rev1.csv (download)
Fig.6D Fig6D/fig6D.m (Main script)
Rawdata/Workspaces/scores_03242014.mat (download)
Fig.7B Fig7/analysis_median_iqr_rotation.m (Main script)
Rawdata/fixedcell/*.* (download)
Fig. 7C, S7A, S7B Fig7/plot_inhib_effect.m (Main script)
Rawdata/fixedcell/*.* (download)
Fig. 7D, S7E, S7F Fig7/run_sensitivity.m (Main script)
Rawdata/fixedcell/*.* (download)
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