Partially interacted phosphorylation/dephosphorylation trees extracted from signaling pathways in cells

Abstract

In order to reconstruct a network that consists of partially interacted phosphorylation/dephosphorylation pathways, combinatorial operations are designed based on the binary phosphorylation/dephosphorylation trees. By using these operations, a polynomial time complexity can be achieved from the bottom-up processes of interacted phosphorylation/dephosphorylation trees. To study the signaling mechanism of cell communication in terms of information theory, a kind of code describing the structure of partially interacted phosphorylation/dephosphorylation trees are also proposed.