Name: sampattavanich-cellsyst-2018
Owner: sorgerlab
Description: Source code for the article "Encoding growth factor identity in the temporal dynamics of a transcription factor under combinatorial regulation" by Sampattavanich et al.
Created: 2018-03-07 15:23:05.0
Updated: 2018-03-16 09:29:38.0
Pushed: 2018-03-16 09:29:36.0
Size: 14796
Language: Matlab
GitHub Committers
| User | Most Recent Commit | # Commits |
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Other Committers
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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) |