Abstract
A recurring set of small sub-networks have been identified as the building blocks of biological networks across diverse organisms. These network motifs have been associated with certain dynamical behaviors and define key modules that are important for understanding complex biological programs. Besides studying the properties of motifs in isolation, existing algorithms often evaluate the occurrence frequency of a specific motif in a given biological network compared to that in random networks of similar structure. However, it remains challenging to relate the structure of motifs to the observed and expected behavior of the larger network. Indeed, even the precise structure of these biological networks remains largely unknown. Previously, we developed a formal reasoning approach enabling the synthesis of biological networks capable of reproducing some experimentally observed behavior. Here, we extend this approach to allow reasoning about the requirement for specific network motifs as a way of explaining how these behaviors arise. We illustrate the approach by analyzing the motifs involved in sign-sensitive delay and pulse generation. We demonstrate the scalability and biological relevance of the approach by revealing the requirement for certain motifs in the network governing stem cell pluripotency.
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Notes
- 1.
While, in general, the motif assignment \(\theta \) is not invertible, \(\theta ^{-1}(c)\) and \(\theta ^{-1}(c')\) can be defined for the interactions \((c,c',*) \in I_{\mathcal {A}, \theta , \mathcal {M}}\) and \((c,c',*) \in I^?_{\mathcal {A}, \theta , \mathcal {M}}\).
- 2.
Depending on the exact implementation, the delay can be observed when the signal switches from active to inactive instead, but this variation of a sign-sensitive delay is not considered here.
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Kugler, H., Dunn, SJ., Yordanov, B. (2018). Formal Analysis of Network Motifs. In: Češka, M., Šafránek, D. (eds) Computational Methods in Systems Biology. CMSB 2018. Lecture Notes in Computer Science(), vol 11095. Springer, Cham. https://doi.org/10.1007/978-3-319-99429-1_7
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