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Network analysis and visualization

SG Shishir K. Gupta
MS Mugdha Srivastava
ÖO Özge Osmanoglu
TD Thomas Dandekar
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The C. floridanus interactome was subjected to topological analysis using Network Analyzer plugin version 2.7 of Cytoscape version 2.8.173. The node degree distribution, mean path length, network diameter and betweenness centrality (BC) were determined with graph theoretic analysis implemented with CentiScaPe74. For the network G(V,E), the BC of node n is defined as follows

here s and t are network nodes different from node n, σst is the number of shortest paths from s to t, and σst (n) gives the number of shortest paths from s to t that goes through node n.

Hubs and bottlenecks in the network were identified with cytoHubba75. Hubs were defined as proteins connecting with ≥5 proteins. Moreover, top 20% of bottlenecks and hubs were considered for mapping of the RNASeq expression data which was collected from our previous publication3.

Copyright and License information: The Author(s) ©2020
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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