StrongestPath: a Cytoscape application for protein–protein interaction analysis

Background StrongestPath is a Cytoscape 3 application that enables to look for one or more cascades of interactions connecting two single or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, it is able to process them and identify the cascade of interactions having the highest total confidence score. Given a set of proteins, StrongestPath can extract and show the network of interactions among them from the given databases, and expand the network by adding new proteins having the most interactions with highest total confidence to the current proteins. The application can also identify any activation or inhibition regulatory paths between two distinct sets of transcription factors and target genes. This application can be either used with a set of built-in human and mouse PPI or signaling databases, or any user-provided database for some organism. Results Our results on 12 signaling pathways from the NetPath database demonstrate that the application can be used for indicating proteins which may play significant roles in the middle of the pathway by finding the strongest path(s) in the PPI or signaling network. Conclusion Easy access to multiple public large databases, generating output in a short time, addressing some key challenges in one platform and providing a user-friendly graphical interface make the StrongestPath easy to use.

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