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Fig. 1 | BMC Systems Biology

Fig. 1

From: Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone

Fig. 1

General representation of the pathway crosstalk perturbation network (PXPN) model. Panel a shows a pathway, a directed graph composed of nodes representing biomolecules and edges representing interactions between them that lead to a biological function. The set of nodes in a pathway is analogous to a gene set. Panel b shows an example of a pathway crosstalk in which two pathways that are involved in different biological functions share a molecule. Panel c shows a pathway crosstalk network (PXN) containing all pathways in a pathway collection and the links between pathways that crosstalk with one another (that is, pathways that have a nonempty intersection). Panel d shows a schematic representation of an enrichment analysis in which data from two different biological states and a list of pathways are taken by an enrichment function, which returns a list of pathways considered to be enriched. Finally, panel E shows the PXPN model in which an enrichment function takes data from two biological states and the set of nodes and edges that define a PXN and returns a network composed by enriched pathways and enriched crosstalk regions

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