StrongestPath: a Cytoscape application for protein–protein interaction analysis

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.

Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with different rooting depth responses to drought stress in potato

“…To identify the hub genes in the eight modules, gene regulatory networks were visualized using Cytoscape software to identify the highly connected genes in the modules ( Doncheva et al., 2019 ; Mousavian et al., 2021 ) ( Figure 6 ). In a network, each node represents a gene, and lines connect the nodes, with genes at either end of a line usually involved in the same biological pathways ( Mousavian et al., 2021 ). In C16, five nuclear genes were examined in the red module, six in the salmon module, seven in the turquoise module, and four in the yellow module.…”

A protein signature associated with active tuberculosis identified by plasma profiling and network-based analysis

“…Although these proteins have not been included in protein signatures before, they have been associated with TB (34-37) and could potentially be generated via similar signaling pathways in response to mycobacterial infection, such as has been indicated for signal transducer and activator of transcription 1 (STAT1) in TB (38). To assess if this was the case, we used the StrongestPath application (39) in Cytoscape to evaluate how the proteins were connected to different STAT transcription factors based on data from the KEGG database (Figure S11). We observed that several of the proteins were directly associated with STAT1, consistent with previous literature (38) to a lesser extent with STAT3 and STAT4, and indirectly with STAT2 and STAT5A.…”

Sequence, structure, and function of the Dps DNA-binding protein from Deinococcus wulumuqiensis R12

“…The number of sequences of the differentially expressed-proteins screened according to the fold change over 1.5 in different comparison groups was compared with the protein network of the STRING database (v.11.0), and the interaction of the partners of the differentially expressed proteins were extracted according to a confidence score > 0.7 (high confidence). “Cytoscape 3.8.2” software was used to visualize the interaction network of differentially expressed proteins [ 29 ]. The “network.links.txt” was imported into Cytoscape.…”