CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks

Tang, Yu; Li, Min; Wang, Jianxin; Pan, Yi; Wu, Fang‐Xiang

doi:10.1016/j.biosystems.2014.11.005

Cited by 937 publications

(651 citation statements)

References 22 publications

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“…PPI networks were visualized and analyzed using the software platform Cytoscape 3.2.1 with the plugins MCODE for cluster analysis and BinGO for gene ontology analysis of protein clusters (37)(38)(39). Global network topological analysis, including clustering coefficients, average number of neighbors (degree), and network heterogeneity as well as local network analysis using betweenness centrality value calculation were carried out with NetworkAnalyzer and the Cytoscape plugin CytoNCA (40,41). The edges in all PPI networks were treated as undirected.…”

Section: Methodsmentioning

confidence: 99%

Biological Relevance and Therapeutic Potential of the Hypusine Modification System

Pällmann

Braig

Sievert

et al. 2015

Journal of Biological Chemistry

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Background: Hypusine modification of the eukaryotic initiation factor 5A (eIF-5A) represents a conserved post-translational modification that regulates translation. Results: Deletion of hypusine modification enzymes exerts strong phenotypes. eIF-5A2-deleted animals are viable and fertile. Conclusion: Both enzymatic steps of hypusine modification are essential for mammalian homeostasis, whereas the cancerrelated isoform eIF-5A2 is dispensable. Significance: eIF-5A2 might represent a safe therapeutic target.

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Section: Methodsmentioning

confidence: 99%

Biological Relevance and Therapeutic Potential of the Hypusine Modification System

Pällmann

Braig

Sievert

et al. 2015

Journal of Biological Chemistry

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“…We used a plugin to Cytoscape called "cytoNCA" [24] and CentriBin [20] to determine the centrality values. The distributions of the centrality values are shown in Fig.…”

Section: Results and Discussion A Determination And Normalization Ofmentioning

confidence: 99%

“…It can be extended through Cytoscape plug-ins. In this work we use Cytoscape ver.3.4.0 integrated with CytoNCA plug-ins [24] to calculate SC. In case of DC, CC, BC, and EC, we calculate the centrality values by utilizing CentriBin [20].…”

Section: Calculation Of Centralitiesmentioning

confidence: 99%

[Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]Centrality Values of Yeast Proteins in a PPI Network Are Related to Their Essentiality and Functions

Altaf‐Ul‐Amin¹,

Wijaya²,

Chandra³

et al. 2017

J. Comput. Aided Chem.

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It has long been investigated and understood that centrality of proteins in the context of protein-protein interaction (PPI) networks are related to their essentiality. In the present work, we validate the relations between essentiality of yeast proteins and their centrality measures in a PPI network by following a different approach using the concept of the receiver operating characteristic (ROC) curve. We found that all centrality measures are related to essentiality. However, the degree centrality performed better in case of the data we used. By deeply examining different centrality values of yeast proteins we find that they are not highly correlated, which has leaded us to hypothesize that centralities might have some relations with gene/protein functions. Indeed, we found that many of the clusters generated based on the pattern of centrality values are rich with similar function proteins. Different types of centrality values imply different types of importance of a node in a network and the functions of genes are of various types. In the present work, we hypothesized that important genes of different functions may tend to show different patterns of centralities and here we show some preliminary links between groups of similar function genes and profiles of centrality values. The concepts of network biology discussed in this paper are applicable to other networks including networks of chemical compounds.

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“…This has been frequently used in many previous studies to represent precision of positive prediction (Deng et al, 2011;Hsing et al, 2008;Li et al, 2011a;Tang et al, 2015). In this work, each set of essential genes or drug targets is used for Ω.…”

Section: Identification Performance Of Functionally Important Genesmentioning

confidence: 99%

Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks

Trinh

Kwon

2015

Biosystems

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CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks

Cited by 937 publications

References 22 publications

Biological Relevance and Therapeutic Potential of the Hypusine Modification System

Biological Relevance and Therapeutic Potential of the Hypusine Modification System

[Dedicated to Prof. T. Okada and Prof. T. Nishioka: data science in chemistry]Centrality Values of Yeast Proteins in a PPI Network Are Related to Their Essentiality and Functions

Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks

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