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NAViGaTOR specifications

Information


Unique identifier OMICS_04115
Name NAViGaTOR
Alternative name Network Analysis, Visualization, & Graphing TORonto
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Network Analysis, Visualization, & Graphing TORonto

NAViGaTOR citations

 (10)
library_books

HABP2 p.G534E variant in patients with family history of thyroid and breast cancer

2017
Oncotarget
PMCID: 5522276
PMID: 28402931
DOI: 10.18632/oncotarget.16639

[…] 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 […]

library_books

Quantification of angiotensin II regulated proteins in urine of patients with polycystic and other chronic kidney diseases by selected reaction monitoring

2016
PMCID: 4974759
PMID: 27499720
DOI: 10.1186/s12014-016-9117-x

[…] 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 […]

library_books

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta analysis of Cancer Gene Signatures and Chemogenomic Data

2015
PLoS Comput Biol
PMCID: 4364883
PMID: 25786242
DOI: 10.1371/journal.pcbi.1004068

[…] 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 […]

library_books

Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis?

2014
Hum Mol Genet
PMCID: 3990162
PMID: 24403051
DOI: 10.1093/hmg/ddt657

[…] 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 […]

library_books

An Integrative Genomic and Transcriptomic Analysis Reveals Potential Targets Associated with Cell Proliferation in Uterine Leiomyomas

2013
PLoS One
PMCID: 3587425
PMID: 23483937
DOI: 10.1371/journal.pone.0057901

[…] 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 […]

library_books

Visualization of protein interaction networks: problems and solutions

2013
BMC Bioinformatics
PMCID: 3548679
PMID: 23368786
DOI: 10.1186/1471-2105-14-S1-S1

[…] 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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NAViGaTOR institution(s)
Division of Signaling Biology, Ontario Cancer Institute and University Health Network, Toronto, ON

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