Logic Modeling Datasets #18
Description
The Saez-Rodriguez group has spent years building logic models of signaling pathways and disease pathways. They have also connected their work to experimental data. Is there a good dataset from that group that could provide (a) experimental data and (b) a logic model, one of which could be SPRAS inputs and the other could be a ground truth dataset? I do not have an obvious direction here, but some papers come to mind:
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The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data (PLOS CompBio, 2009). This is the paper that made me think of this direction. The paper builds a logic model of EGFR signaling, then analyzes phosphorylation status of cells treated with TGFalpha (which turns on the pathway) and seven small-molecule drugs where six inhibit the activation of nodes in the model. The paper evaluates how well the Boolean model mirrors the experimental outputs.
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Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis (Genome Medicine 2021). Network-based modeling based on phosphoproteomic data to uncover differential activation between healthy donors, untreated patients, and patients undergoing different treatments. The supplement includes a list of interactions in the prior knowledge network and phosphoproteins that are involved in pathways associated with MS.