Experimente

Selection of experiments

To select experiments to be reproduced in the COMBINE archive, we initially reviewed the paper by Bachmann et al. [1]. It contains six main figures as well as >60 figures in the supplementary information. Any figures showing only experimental data such as immunoblotting (e.g., Figure 1) or model maps (e.g., Figure 2) were immediately excluded. From the remaining (sub-)figures we selected those containing model simulations (e.g., Figure 4).

The following table lists the figures which were (partially) reproduced:

Figure		Status	Comment/Problems
1	Phosphorylation profile of Epo-induced EpoR-JAK2-STAT5 signaling in the presence and absence of actinomycin D.	not selected
2	Mathematical model of dual negative feedback regulation of JAK2-STAT5 signaling.	not selected
3	Model calibration with experimental data of JAK2-STAT5 signaling obtained by different experimental techniques.	partially reproduced	tSTAT5 not defined in model
4	Experimental data of JAK2-STAT5 signaling under perturbed conditions used for model calibration.	partially reproduced	pJAK2, pEPOR, SHP1oe not defined in model
5	Linking the integral response of phosphorylated STAT5 in the nucleus to the survival rate of CFU-E cells.	Fig5A partially reproduced	unclear how to simulate Epo level
6	Dual negative feedback with divided function in JAK2-STAT5 signaling.	Fig6A not reproduced	unclear how to simulate knockout and Epo level
S9	Simulation of the effect of extrinsic noise on the model dynamics	reproduced

Reference

[1] Bachmann, J. et al. Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range. Molecular Systems Biology 7, 516 (2011). https://doi.org/10.1038/msb.2011.50