StrongestPath: a Cytoscape application for protein–protein interaction analysis

• Main Authors: Zaynab Mousavian, Mehran Khodabandeh, Ali Sharifi-Zarchi, Alireza Nadafian, Alireza Mahmoudi
• Format: Article
• Language: English
• Published: BMC 2021-06-01
• Series: BMC Bioinformatics
• Subjects: Protein–protein interaction network; Signaling network; Pathway reconstruction; Regulatory pathway; Cytoscape App
• Online Access: https://doi.org/10.1186/s12859-021-04230-4

Abstract Background StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins 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, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can also identify any activating or inhibitory regulatory paths between two distinct sets of transcription factors and target genes. This application can be used on the 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 a 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 StrongestPath an extremely useful application.