Computational protocol: Uncovering potential Drug Targets for Tuberculosis using Protein Networks

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Protocol publication

[…] The interacting partners of all the 141 reported protein targets were selected from the STRING database and a network was constructed with Cytoscape 2.8.0 [], a network visualization and analysis software. The shortest paths between all pairs of proteins in the network were computed. For every node in a network, the Network Analyzer computes its degree, its clustering coefficient, the number of self-loops, and a variety of other parameters. ClusterOne plugin used on the network strives to discover densely connected and possibly overlapping regions within the Cytoscape network. It essentially looks for groups of high cohesiveness based on the parameters, minimum size, minimum density, edge weights, merging and seeding methods. The minimum size of the cluster for all the proteins in the network was set to 15 resulting in 19 clusters ().The minimum sizes for the individual networks were set to 7. The highly interacting nodes in the cluster was identified by molecular complex detection (MCODE) algorithm [], by keeping K-Core =4 - 8, node score cutoff = 0.2 and max depth up to 100. At each level topological properties were studied to justify the important nodes/hubs playing crucial role in the functional pathways of the TB bacterium. […]

Pipeline specifications

Software tools ClusterONE, MCODE
Application Protein interaction analysis
Diseases Communicable Diseases, Tuberculosis, Tuberculosis, Meningeal, HIV Infections