This webpage provides access to Computing Code developed for the following paper:
Schütte et al “An experimentally validated network of 9 haematopoietic transcription factors reveals mechanisms of cell state stability” eLife in press.
This paper reports comprehensive ChIP-Seq, transgenic and reporter gene experimental data that were used to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell gene expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic transcription factor (TF) fusion protein perturbs key HSPC regulators.
The Matlab codes include three modules:
1) In silico model
2) Simplified model
3) Exponents changed model
As explained in the Material and Methods section, the exponents changed model refers to the setting where the exponents in equations change less than linearly along with the increase in the number of motifs.
To run simulations using any of the three models listed above:
First, change Current Folder of MATLAB to ‘in silico model’, or ’Simplified model’, or ’Probabilities changed model’.
Second, type in Command Window:
run single_run
% simulate the expression of a single wild-type cell over 50 discrete time points. Output is a 50x9 matrix named as ‘output’.
run multiple_run
% simulate the overall distributions of the expression of all nine TFs as might be seen in a cell population by implementing 1000 independent simulations. Each simulation has 50 discrete time points. A single time point (sample) is randomly drawn from each simulation after the first 10 time points (burn-in period used to secure the reach of stabilisation). The selected samples form together a pool of 1000 simulated single cells, which are used to derive the overall distributions of the expression for all nine TFs. Please note that all perturbation simulations mentioned below follow the same subsampling strategy as described here. Output is a 1000x9 matrix named as ‘matrix_wildtype’, or ‘matrix_wildtype_sm’, or ‘matrix_wildtype_ex’.
run down_PU.1/Spi1
% simulate complete removal of PU.1/Spi1 after the model has reached its initial steady state. Output is a 1000x9 matrix named as ‘matrix_down_PU1’, or ‘matrix_down_PU1_sm’, or ‘matrix_down_PU1_ex’.
run up_Gfi1b
% simulate Gfi1b overexpression by increasing the expression level of Gfi1b to the hypothetical maximum level 1 after the model has reached its initial steady state. Output is a 1000x9 matrix named as ‘matrix_up_Gfi1b’, or ‘matrix_up_Gfi1b_sm’, or ‘matrix_up_Gfi1b_ex’.
run down_Scl/Tal1
% simulate complete removal of Scl/Tal1 after the model has reached its initial steady state. Output is a 1000x9 matrix named as ‘matrix_down_Scl’ or ‘matrix_down_Scl_sm’.
run down_Lyl1
% simulate complete removal of Lyl1 after the model has reached its initial steady state. Output is a 1000x9 matrix named as ‘matrix_down_Lyl1’ or ‘matrix_down_Lyl1_sm’.
run down_SclLyl1
% simulate simultaneous complete removal of Scl/Tal1 and Lyl1 after the model has reached its initial steady state. Output is a 1000x9 matrix named as ‘matrix_down_SclLyl1’ or ‘matrix_down_SclLyl1_sm’.
run up_Runx1_AE
% simulate the leukaemic scenario caused by AML-ETO9a expression. The level of Runx1 is fixed at the hypothetical maximum level 1, and at the same time all activating inputs of Runx1 are converted to inhibiting inputs in the model. Output is a 1000x9 matrix named as ‘matrix_up_Runx1_AE’, or ‘matrix_up_Runx1_AE_ex’.
Third, any distribution fitting techniques can subsequently be applied to the outputs to produce desired plots.
