Here is some use case as provided by Sujatha & Malabika Sarkar
E2 (estrogen) induced phosphorylation of STAT5A, STAT5B and STAT3
Serine Phosphorylation of Stat5 Is Required for Optimal Transcriptional Activity in Response to 17ß-Estradiol.
In addition to tyrosine phosphorylation, serine phosphorylation of Stat5 was also rapidly induced by 17ß-estradiol (Fig. 1A). Together with the establishment of serine phosphorylation as a regulator of Stat5 transcriptional activity in T lymphocytes (34), this observation prompted us to analyze the importance of specific serine residues within Stat5 for 17ß-estradiol-induced activation of the ß-casein promoter. Stat5ab-/- cells were transiently transfected with wild-type Stat5a or different point mutants, in which serine residues 725 and/or 779 in the C-terminal transactivation domain had been changed to alanines (S725A, S779A, and S725/779) (35), together with the ß-casein reporter gene and NLSA. Interestingly, the S725A, S779A, and S725/779A mutants all showed a lower induction of the reporter in response to 17ß-estradiol compared with wild-type Stat5a (Fig. 7). As expected, the Y694F mutant, in which the critical tyrosine residue 694 had been changed to phenylalanine, was unable to induce activation above basal level (Fig. 7). In conclusion, these results demonstrate that tyrosine phosphorylation is a prerequisite for 17ß- estradiol-induced transactivation of Stat5a, whereas intact serine residues in the transactivation domain are important for optimal transcriptional activity.
Stat3 Is Activated by the 17ß-Estradiol-Induced Pathway
The observation that Stat5 was not the only transcription factor responsible for activating the ß-casein promoter in response to 17ß-estradiol prompted us to test the involvement of other Stat family members with similar characteristics. In a DNA-binding assay, Stat3 was found to bind to the consensus {gamma}-interferon-activated sequence element present in the ß-casein promoter in vitro (data not shown) and, furthermore, Stat3 was shown to activate the ß-casein reporter gene in transient transfection experiments (data not shown and Ref. 27). The phosphorylation status of Stat3 upon 50 nM 17ß-estradiol or 15% serum (FBS) treatment was analyzed by Western blot analyses of PAE whole-cell extracts, using phospho-specific antibodies against tyrosine-705 and serine-727 of Stat3, respectively. As shown in Fig. 4A, both tyrosine and serine phosphorylation of Stat3 were induced within 15 min of 17ß-estradiol treatment and were inhibited in the presence of ICI 182,780. Total levels of Stat3 protein in the cell extracts are shown in Fig. 4A (lower panel).
The catch is there is an unknown pathway which ultimately activates phosphorylation of both Stat3 and Stat5. One way to show this in BioPAX is to use control class to show an indirect control. However if there are multiple activators of this pathway ( and indeed there are although not listed in the above abstracts) it can need n*m control relations which is a bit of a mess. Besided it might have been nice to have a blackbox estrogen pathway as a placeholder for future curation.
Thus, I would like to express it in this form:
17B-Estradiol -<controls>-> Estrogen induced pathway -<controls>->Phosphorylation of Stat 3 and 5
It is almost possible to represent this in BioPAX, however second control is problemmatic. Since controller property requires a PEP
Now this is meaningful in level 2, since you need a PEP to capture state information ( location and modifications ). However stochiometry for a controller does not really make sense. This was extensively discussed in the SBML list as well. So for level 3 I propose to change the domain of the controller property to state or physical entity or pathway, which also solves the above problem.