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|Alternative name||Network Analysis, Visualization, & Graphing TORonto|
|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
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Publication for Network Analysis, Visualization, & Graphing TORonto
HABP2 p.G534E variant in patients with family history of thyroid and breast cancer
[…] ntify biological context by querying protein-protein interaction (PPI) database Interologous Interaction Database v. 2016-03  (http://ophid.utoronto.ca/iid). The resulting network was visualized in NAViGaTOR v3  (http://ophid.utoronto.ca/navigator).To elucidate biological functions of the protein network (Figure ), we performed a comprehensive pathway enrichment analysis. The Pathway Data Inte […]
Quantification of angiotensin II regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring
[…] ated partners (including orthologous interaction evidence). Ang II-regulated proteins and their PPI partners were then subjected to pathway enrichment analysis. Resulting network was visualized using NAViGaTOR v 2.3 (http://ophid.utoronto.ca/navigator) (1937718), and the corresponding XML file can be found at: http://www.cs.utoronto.ca/~juris/data/ClinProteom16/.Considering the proteins in the net […]
Prioritizing Therapeutics for Lung Cancer: An Integrative Meta analysis of Cancer Gene Signatures and Chemogenomic Data
[…] 133A probeset IDs for Connectivity Map analysis using the hgu133a.db (Bioconductor 2.8). The drug-target and mode of action networks were analyzed using igraph (Bioconductor 2.8) and visualized using NAViGaTOR 2.3.2 , and drug structures were visualized with PyMOL . We calculated Tanimoto similarity for all pairs of 1,148 CMap drugs for which PubChem IDs were available using the PubChem Chemic […]
Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis?
[…] hsa-miR-21, has-miR-345 and has-miR-281b) of oral leukoplakia progression using the same samples described herein for aCGH profiling (), we sought to integrate PPI networks of genes and miRNAs. Using NAViGaTOR (), we combined the network from Supplementary Material, Figure S2 with a network from proteins that correspond to targets of the 3-miRNA signature. This network-based integrative analysis i […]
An Integrative Genomic and Transcriptomic Analysis Reveals Potential Targets Associated with Cell Proliferation in Uterine Leiomyomas
[…] s performed using known and predicted physical protein-protein interactions from I2D version 2.0 (http://ophid.utoronto.ca/i2d) . Visualisation and analysis of the resulting network were conducted in NAViGaTOR version 2.3 (http://ophid.utoronto.ca/navigator) . Briefly, to generate a list of the target proteins, we extracted all of the interacting partners from I2D and mapped the interactions among […]
Visualization of protein interaction networks: problems and solutions
[…] course analysis of the networks in addition to cluster analysis. BioLayoutExpres3D allows the user to make complex analysis, as clustering, mining of genes and Petri-Net simulation. Finally, Medusa, NAViGaTOR, and Pajek allow the user to make clustering analysis. Many times, the user has to manually combine different tools to conduct complex analysis on graphs obtained in previous analysis. The c […]
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