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plakrisenko merged 8 commits into from
Nov 13, 2025
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Lucarelli visualization #286

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15d9f2e
Lucarelli visualization
plakrisenko Oct 31, 2025
d71bd1b
fix yaml
plakrisenko Oct 31, 2025
cbcf706
fig1, D, right plots
plakrisenko Nov 1, 2025
06cef8d
add multiple visualization files
plakrisenko Nov 6, 2025
36b0b23
finish visualization specification
plakrisenko Nov 6, 2025
5fffd72
add title
plakrisenko Nov 10, 2025
fec684f
fix information about paper figures
plakrisenko Nov 11, 2025
5c0ec4c
fix information about paper figures
plakrisenko Nov 11, 2025
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2 changes: 2 additions & 0 deletions Benchmark-Models/Lucarelli_CellSystems2018/Lucarelli_CellSystems2018.yaml
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- observables_Lucarelli_CellSystems2018.tsv
sbml_files:
- model_Lucarelli_CellSystems2018.xml
visualization_files:
- visualizationSpecification_Lucarelli_CellSystems2018.tsv
3,512 changes: 1,756 additions & 1,756 deletions Benchmark-Models/Lucarelli_CellSystems2018/measurementData_Lucarelli_CellSystems2018.tsv
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3,512 changes: 1,756 additions & 1,756 deletions Benchmark-Models/Lucarelli_CellSystems2018/simulatedData_Lucarelli_CellSystems2018.tsv
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156 changes: 156 additions & 0 deletions ...Models/Lucarelli_CellSystems2018/visualizationSpecification_Lucarelli_CellSystems2018.tsv
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23 changes: 23 additions & 0 deletions ...ucarelli_CellSystems2018/visualizationSpecification_Lucarelli_CellSystems2018_Figure1.tsv
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plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset datasetId paperFigure
Fig1A MeanAndSD Smad2/4 abundance BarPlot lin molecules/cell (x10$^4$) lin Smad2 S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 time 0 0 smad24_abundance fig1, A
Fig1A MeanAndSD Smad2/4 abundance BarPlot lin molecules/cell (x10$^4$) lin Smad4 S4IP_tS4_MSPL2_PL_PN_molecules_per_cell_hepa16_nExpID1 time 0 0 smad24_abundance fig1, A
Fig1B MeanAndSD Smad2/3 isoform abundance LinePlot time [min] lin molecules/cell (x10$^4$) lin Smad2 S23IP_tS2_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 time 0 0 isoform_abundance fig1, B
Fig1B MeanAndSD Smad2/3 isoform abundance LinePlot time [min] lin molecules/cell (x10$^4$) lin Smad3 S23IP_tS3_MSPL2_PL_PN_molecules_per_cell_hepa16_ratios_nExpID10 time 0 0 isoform_abundance fig1, B
Fig1C_1 MeanAndSD Smad2 phosphorylation LinePlot time [min] lin molecules/cell (x10$^4$) lin nSmad2 S23IP_S2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 time 0 0 smad2_phosphorylation fig1, C
Fig1C_1 MeanAndSD Smad2 phosphorylation LinePlot time [min] lin molecules/cell (x10$^4$) lin pSmad2 S23IP_pS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 time 0 0 smad2_phosphorylation fig1, C
Fig1C_1 MeanAndSD Smad2 phosphorylation LinePlot time [min] lin molecules/cell (x10$^4$) lin ppSmad2 S23IP_ppS2_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 time 0 0 smad2_phosphorylation fig1, C
Fig1C_2 MeanAndSD Smad3 phosphorylation LinePlot time [min] lin molecules/cell (x10$^4$) lin nSmad3 S23IP_S3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 time 0 0 smad3_phosphorylation fig1, C
Fig1C_2 MeanAndSD Smad3 phosphorylation LinePlot time [min] lin molecules/cell (x10$^4$) lin pSmad3 S23IP_pS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 time 0 0 smad3_phosphorylation fig1, C
Fig1C_2 MeanAndSD Smad3 phosphorylation LinePlot time [min] lin molecules/cell (x10$^4$) lin ppSmad3 S23IP_ppS3_MSPL2_PL_hepa16_pS2_pS3_time_course_nExpID5 time 0 0 smad3_phosphorylation fig1, C
Fig1D_1 MeanAndSD Smad2 IP BarPlot lin molecules/cell (x10$^4$) lin nSmad2 S2IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad2IP fig1, left
Fig1D_1 MeanAndSD Smad2 IP BarPlot lin molecules/cell (x10$^4$) lin pSmad2 S2IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad2IP fig1, left
Fig1D_1 MeanAndSD Smad2 IP BarPlot lin molecules/cell (x10$^4$) lin ppSmad2 S2IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad2IP fig1, left
Fig1D_1 MeanAndSD Smad2 IP BarPlot lin molecules/cell (x10$^4$) lin nSmad3 S2IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad2IP fig1, left
Fig1D_1 MeanAndSD Smad2 IP BarPlot lin molecules/cell (x10$^4$) lin pSmad3 S2IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad2IP fig1, left
Fig1D_1 MeanAndSD Smad2 IP BarPlot lin molecules/cell (x10$^4$) lin ppSmad3 S2IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad2IP fig1, left
Fig1D_2 MeanAndSD Smad3 IP BarPlot lin molecules/cell (x10$^4$) lin nSmad3 S3IP_S3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad3IP fig1, right
Fig1D_2 MeanAndSD Smad3 IP BarPlot lin molecules/cell (x10$^4$) lin pSmad3 S3IP_pS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad3IP fig1, right
Fig1D_2 MeanAndSD Smad3 IP BarPlot lin molecules/cell (x10$^4$) lin ppSmad3 S3IP_ppS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad3IP fig1, right
Fig1D_2 MeanAndSD Smad3 IP BarPlot lin molecules/cell (x10$^4$) lin nSmad2 S3IP_S2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad3IP fig1, right
Fig1D_2 MeanAndSD Smad3 IP BarPlot lin molecules/cell (x10$^4$) lin pSmad2 S3IP_pS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad3IP fig1, right
Fig1D_2 MeanAndSD Smad3 IP BarPlot lin molecules/cell (x10$^4$) lin ppSmad2 S3IP_ppS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 time 0 0 Smad3IP fig1, right
22 changes: 22 additions & 0 deletions ...ucarelli_CellSystems2018/visualizationSpecification_Lucarelli_CellSystems2018_Figure2.tsv
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plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset datasetId paperFigure
Fig2D_right_1 MeanAndSD Smad2 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad2 S2IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset1 fig2, D, right
Fig2D_right_1 MeanAndSD Smad2 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad3 S2IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset2 fig2, D, right
Fig2D_right_1 MeanAndSD Smad2 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad4 S2IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset3 fig2, D, right
Fig2D_right_2 MeanAndSD Smad3 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad2 S3IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset4 fig2, D, right
Fig2D_right_2 MeanAndSD Smad3 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad3 S3IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset5 fig2, D, right
Fig2D_right_2 MeanAndSD Smad3 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad4 S3IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset6 fig2, D, right
Fig2D_right_3 MeanAndSD Smad4 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad2 S4IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset7 fig2, D, right
Fig2D_right_3 MeanAndSD Smad4 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad3 S4IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset8 fig2, D, right
Fig2D_right_3 MeanAndSD Smad4 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad4 S4IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset9 fig2, D, right
Fig2D_right_4 MeanAndSD Smad2/3 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad2 S23IP_tS2_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset10 fig2, D, right
Fig2D_right_4 MeanAndSD Smad2/3 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad3 S23IP_tS3_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset11 fig2, D, right
Fig2D_right_4 MeanAndSD Smad2/3 IP LinePlot TGF$\beta$ (ng/ml) lin relative abundance [%] lin Smad4 S23IP_tS4_MSPL2_complexes_all_hepa16_no_single_complex_nExpID2 init_TGFb 0 0 dataset12 fig2, D, right
Fig2D_left_1 MeanAndSD Smad2 IP LinePlot time [min] lin relative abundance [%] lin Smad2 S2IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_1 MeanAndSD Smad2 IP LinePlot time [min] lin relative abundance [%] lin Smad3 S2IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_1 MeanAndSD Smad2 IP LinePlot time [min] lin relative abundance [%] lin Smad4 S2IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_2 MeanAndSD Smad3 IP LinePlot time [min] lin relative abundance [%] lin Smad2 S3IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_2 MeanAndSD Smad3 IP LinePlot time [min] lin relative abundance [%] lin Smad3 S3IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_2 MeanAndSD Smad3 IP LinePlot time [min] lin relative abundance [%] lin Smad4 S3IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_3 MeanAndSD Smad4 IP LinePlot time [min] lin relative abundance [%] lin Smad2 S4IP_tS2_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_3 MeanAndSD Smad4 IP LinePlot time [min] lin relative abundance [%] lin Smad3 S4IP_tS3_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
Fig2D_left_3 MeanAndSD Smad4 IP LinePlot time [min] lin relative abundance [%] lin Smad4 S4IP_tS4_MSPL2_complexes_all_hepa16_time_course_nExpID6 time 0 0 fig2Dleft fig2, D, left
25 changes: 25 additions & 0 deletions ...arelli_CellSystems2018/visualizationSpecification_Lucarelli_CellSystems2018_Figure3_1.tsv
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plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset datasetId paperFigure
Fig3F_Ski_1 MeanAndSD Ski LinePlot time [min] lin gene expression (log) log10 untreated Ski_gene_expression_OE_nExpID100 time 0 0 Ski_gene_expression1 fig3, F
Fig3F_Ski_1 MeanAndSD Ski LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Ski_gene_expression_OE_nExpID100 time 0 0 Ski_gene_expression1_tgf fig3, F
Fig3F_Skil_1 MeanAndSD Skil LinePlot time [min] lin gene expression (log) log10 untreated Skil_gene_expression_OE_nExpID100 time 0 0 Skil_gene_expression1 fig3, F
Fig3F_Skil_1 MeanAndSD Skil LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Skil_gene_expression_OE_nExpID100 time 0 0 Skil_gene_expression1_tgf fig3, F
Fig3F_Dnmt3a_1 MeanAndSD Dnmt3a LinePlot time [min] lin gene expression (log) log10 untreated Dnmt3a_gene_expression_OE_nExpID100 time 0 0 Dnmt3a_gene_expression1 fig3, F
Fig3F_Dnmt3a_1 MeanAndSD Dnmt3a LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Dnmt3a_gene_expression_OE_nExpID100 time 0 0 Dnmt3a_gene_expression1_tgf fig3, F
Fig3F_Sox4_1 MeanAndSD Sox4 LinePlot time [min] lin gene expression (log) log10 untreated Sox4_gene_expression_OE_nExpID100 time 0 0 Sox4_gene_expression1 fig3, F
Fig3F_Sox4_1 MeanAndSD Sox4 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Sox4_gene_expression_OE_nExpID100 time 0 0 Sox4_gene_expression1_tgf fig3, F
Fig3F_Jun_1 MeanAndSD Jun LinePlot time [min] lin gene expression (log) log10 untreated Jun_gene_expression_OE_nExpID100 time 0 0 Jun_gene_expression1 fig3, F
Fig3F_Jun_1 MeanAndSD Jun LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Jun_gene_expression_OE_nExpID100 time 0 0 Jun_gene_expression1_tgf fig3, F
Fig3F_Smad7_1 MeanAndSD Smad7 LinePlot time [min] lin gene expression (log) log10 untreated Smad7_gene_expression_OE_nExpID100 time 0 0 Smad7_gene_expression1 fig3, F
Fig3F_Smad7_1 MeanAndSD Smad7 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Smad7_gene_expression_OE_nExpID100 time 0 0 Smad7_gene_expression1_tgf fig3, F
Fig3F_Klf10_1 MeanAndSD Klf10 LinePlot time [min] lin gene expression (log) log10 untreated Klf10_gene_expression_OE_nExpID100 time 0 0 Klf10_gene_expression1 fig3, F
Fig3F_Klf10_1 MeanAndSD Klf10 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Klf10_gene_expression_OE_nExpID100 time 0 0 Klf10_gene_expression1_tgf fig3, F
Fig3F_Bmp4_1 MeanAndSD Bmp4 LinePlot time [min] lin gene expression (log) log10 untreated Bmp4_gene_expression_OE_nExpID100 time 0 0 Bmp4_gene_expression1 fig3, F
Fig3F_Bmp4_1 MeanAndSD Bmp4 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Bmp4_gene_expression_OE_nExpID100 time 0 0 Bmp4_gene_expression1_tgf fig3, F
Fig3F_Cxcl15_1 MeanAndSD Cxcl15 LinePlot time [min] lin gene expression (log) log10 untreated Cxcl15_gene_expression_OE_nExpID100 time 0 0 Cxcl15_gene_expression1 fig3, F
Fig3F_Cxcl15_1 MeanAndSD Cxcl15 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Cxcl15_gene_expression_OE_nExpID100 time 0 0 Cxcl15_gene_expression1_tgf fig3, F
Fig3F_Dusp5_1 MeanAndSD Dusp5 LinePlot time [min] lin gene expression (log) log10 untreated Dusp5_gene_expression_OE_nExpID100 time 0 0 Dusp5_gene_expression1 fig3, F
Fig3F_Dusp5_1 MeanAndSD Dusp5 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Dusp5_gene_expression_OE_nExpID100 time 0 0 Dusp5_gene_expression1_tgf fig3, F
Fig3F_Tgfa_1 MeanAndSD Tgfa LinePlot time [min] lin gene expression (log) log10 untreated Tgfa_gene_expression_OE_nExpID100 time 0 0 Tgfa_gene_expression1 fig3, F
Fig3F_Tgfa_1 MeanAndSD Tgfa LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Tgfa_gene_expression_OE_nExpID100 time 0 0 Tgfa_gene_expression1_tgf fig3, F
Fig3F_Pdk4_1 MeanAndSD Pdk4 LinePlot time [min] lin gene expression (log) log10 untreated Pdk4_gene_expression_OE_nExpID100 time 0 0 Pdk4_gene_expression1 fig3, F
Fig3F_Pdk4_1 MeanAndSD Pdk4 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Pdk4_gene_expression_OE_nExpID100 time 0 0 Pdk4_gene_expression1_tgf fig3, F
25 changes: 25 additions & 0 deletions ...arelli_CellSystems2018/visualizationSpecification_Lucarelli_CellSystems2018_Figure3_2.tsv
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plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset datasetId paperFigure
Fig3F_Ski_2 MeanAndSD Ski LinePlot time [min] lin gene expression (log) log10 untreated Ski_gene_expression_OE_nExpID100 time 0 0 Ski_gene_expression2 fig3, F
Fig3F_Ski_2 MeanAndSD Ski LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Ski_gene_expression_OE_nExpID100 time 0 0 Ski_gene_expression2_tgf fig3, F
Fig3F_Skil_2 MeanAndSD Skil LinePlot time [min] lin gene expression (log) log10 untreated Skil_gene_expression_OE_nExpID100 time 0 0 Skil_gene_expression2 fig3, F
Fig3F_Skil_2 MeanAndSD Skil LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Skil_gene_expression_OE_nExpID100 time 0 0 Skil_gene_expression2_tgf fig3, F
Fig3F_Dnmt3a_2 MeanAndSD Dnmt3a LinePlot time [min] lin gene expression (log) log10 untreated Dnmt3a_gene_expression_OE_nExpID100 time 0 0 Dnmt3a_gene_expression2 fig3, F
Fig3F_Dnmt3a_2 MeanAndSD Dnmt3a LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Dnmt3a_gene_expression_OE_nExpID100 time 0 0 Dnmt3a_gene_expression2_tgf fig3, F
Fig3F_Sox4_2 MeanAndSD Sox4 LinePlot time [min] lin gene expression (log) log10 untreated Sox4_gene_expression_OE_nExpID100 time 0 0 Sox4_gene_expression2 fig3, F
Fig3F_Sox4_2 MeanAndSD Sox4 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Sox4_gene_expression_OE_nExpID100 time 0 0 Sox4_gene_expression2_tgf fig3, F
Fig3F_Jun_2 MeanAndSD Jun LinePlot time [min] lin gene expression (log) log10 untreated Jun_gene_expression_OE_nExpID100 time 0 0 Jun_gene_expression2 fig3, F
Fig3F_Jun_2 MeanAndSD Jun LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Jun_gene_expression_OE_nExpID100 time 0 0 Jun_gene_expression2_tgf fig3, F
Fig3F_Smad7_2 MeanAndSD Smad7 LinePlot time [min] lin gene expression (log) log10 untreated Smad7_gene_expression_OE_nExpID100 time 0 0 Smad7_gene_expression2 fig3, F
Fig3F_Smad7_2 MeanAndSD Smad7 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Smad7_gene_expression_OE_nExpID100 time 0 0 Smad7_gene_expression2_tgf fig3, F
Fig3F_Klf10_2 MeanAndSD Klf10 LinePlot time [min] lin gene expression (log) log10 untreated Klf10_gene_expression_OE_nExpID100 time 0 0 Klf10_gene_expression2 fig3, F
Fig3F_Klf10_2 MeanAndSD Klf10 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Klf10_gene_expression_OE_nExpID100 time 0 0 Klf10_gene_expression2_tgf fig3, F
Fig3F_Bmp4_2 MeanAndSD Bmp4 LinePlot time [min] lin gene expression (log) log10 untreated Bmp4_gene_expression_OE_nExpID100 time 0 0 Bmp4_gene_expression2 fig3, F
Fig3F_Bmp4_2 MeanAndSD Bmp4 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Bmp4_gene_expression_OE_nExpID100 time 0 0 Bmp4_gene_expression2_tgf fig3, F
Fig3F_Cxcl15_2 MeanAndSD Cxcl15 LinePlot time [min] lin gene expression (log) log10 untreated Cxcl15_gene_expression_OE_nExpID100 time 0 0 Cxcl15_gene_expression2 fig3, F
Fig3F_Cxcl15_2 MeanAndSD Cxcl15 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Cxcl15_gene_expression_OE_nExpID100 time 0 0 Cxcl15_gene_expression2_tgf fig3, F
Fig3F_Dusp5_2 MeanAndSD Dusp5 LinePlot time [min] lin gene expression (log) log10 untreated Dusp5_gene_expression_OE_nExpID100 time 0 0 Dusp5_gene_expression2 fig3, F
Fig3F_Dusp5_2 MeanAndSD Dusp5 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Dusp5_gene_expression_OE_nExpID100 time 0 0 Dusp5_gene_expression2_tgf fig3, F
Fig3F_Tgfa_2 MeanAndSD Tgfa LinePlot time [min] lin gene expression (log) log10 untreated Tgfa_gene_expression_OE_nExpID100 time 0 0 Tgfa_gene_expression2 fig3, F
Fig3F_Tgfa_2 MeanAndSD Tgfa LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Tgfa_gene_expression_OE_nExpID100 time 0 0 Tgfa_gene_expression2_tgf fig3, F
Fig3F_Pdk4_2 MeanAndSD Pdk4 LinePlot time [min] lin gene expression (log) log10 untreated Pdk4_gene_expression_OE_nExpID100 time 0 0 Pdk4_gene_expression2 fig3, F
Fig3F_Pdk4_2 MeanAndSD Pdk4 LinePlot time [min] lin gene expression (log) log10 TGF$\beta$-treated Pdk4_gene_expression_OE_nExpID100 time 0 0 Pdk4_gene_expression2_tgf fig3, F
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