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CytoNCA specifications


Unique identifier OMICS_12243
Name CytoNCA
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Medium
Version 2.1.6
Stability Stable
Maintained Yes


No version available



  • person_outline Yu Tang

Publication for CytoNCA

CytoNCA citations


Comprehensive and integrative analysis identifies microRNA 106 as a novel non invasive biomarker for detection of gastric cancer

J Transl Med
PMCID: 5952699
PMID: 29764446
DOI: 10.1186/s12967-018-1510-y

[…] le, we identified several hub genes of miR-106a and miR-106b targets by using three different methods including betweenness centrality, closeness centrality and degree centrality based on the plug-in CytoNCA []. In addition, the significant modules in the PPI network were screened by plug-in Molecular Complex Detection (MCODE) of Cytoscape. As for a further comment, KEGG pathway analysis was perfo […]


Systems pharmacology approach reveals the antiinflammatory effects of Ampelopsis grossedentata on dextran sodium sulfate induced colitis

PMCID: 5889820
PMID: 29632421
DOI: 10.3748/wjg.v24.i13.1398

[…] to confirm the candidate targets of AMP against UC, an intersection of the above networks was conducted, which consisted of 2543 nodes and 70816 edges, and the DC values of 35 and 70 were computed by CytoNCA to identify the putative targets during the process (Figure ).In order to further elucidate the possible effects of AMP on UC, the biological processes and signaling pathways were determined t […]


Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor

PMCID: 5894672
PMID: 29670360
DOI: 10.2147/OTT.S148776

[…] in the PPI network. Three methods including degree centrality, betweenness centrality, and closeness centrality were used to analyze network topological features of nodes in the PPI network using the CytoNCA plug-in ( in Cytoscape software. Hub nodes with higher topology scores were identified. Significant modules (densely connected subnetwork regions) in the […]


Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma

PMCID: 5875410
PMID: 29618931
DOI: 10.2147/OTT.S150565

[…] und, and then the DEGs were mapped into the background to obtain their PPI pairs. Subsequently, the PPI network for the DEGs was visualized by Cytoscape software ( Using the CytoNCA plugin (version 2.1.6, in Cytoscape software, betweenness centrality (BC), degree centrality (DC), and closeness centrality (CC) of the nodes in PPI net […]


Identification of potential key protein interaction networks of BK virus nephropathy in patients receiving kidney transplantation

Sci Rep
PMCID: 5864740
PMID: 29567951
DOI: 10.1038/s41598-018-23492-2

[…] In Cytoscape, scattered proteins were removed from the final PPIs. The hub protein, which interacts most frequently with other proteins and works like a hub in the network, were selected by CytoNCA according to degree centrality, betweenness centrality and subgraph centrality. Finally, proteins associated with hub proteins at the degree ≥10 were selected and constructed the significant n […]


Study of Imidazolium Salt Derivatives as PIK3CA Inhibitors Using a Comprehensive in Silico Method

Int J Mol Sci
PMCID: 5877757
PMID: 29562629
DOI: 10.3390/ijms19030896

[…] ll be combined together to construct the PPI network. The weight of a node in the PPI network was determined by its own properties and its associated edges []; three centrality measures calculated by CytoNCA plugins Subgraph Centrality, Betweenness Centrality and Closeness Centrality [,,] were utilized to generate the sub-network and to screen the potential target of the imidazolium salt derivativ […]

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CytoNCA institution(s)
School of Information Science and Engineering, Central South University, Changsha, China; Department of Computer Science, Georgia State University, Atlanta, GA, USA; Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK, Canada

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