NetBox protocols

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NetBox specifications

Information


Unique identifier OMICS_26187
Name NetBox
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Python
Computer skills Advanced
Version 1.0
Stability Stable
Source code URL http://sanderlab.org/tools/netbox.tar.gz
Maintained Yes

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Maintainer


  • person_outline Ethan Cerami <>

Publication for NetBox

NetBox in pipelines

 (3)
2016
PMCID: 5103929
PMID: 27899990
DOI: 10.3892/ol.2016.5122

[…] but interact with degs, were obtained through mapping degs onto the network. cytoscape software () was used to visualize the molecular interaction. besides the ppi network under the criteria, netbox also divided the network into modules. the modules with the maximum number of nodes in the ppi network were subjected to go terms and swiss-prot and protein information resource keywords […]

2015
PMCID: 4826206
PMID: 26735889
DOI: 10.18632/oncotarget.6774

[…] matrix q = y(yty)−1/2. the spectral clustering plans to minimize the objective function were as follows: minq∈rn×c trace(qtl+q)s.t.qtq=i(8) , the construction of subtype-specific network modules in netbox [] allows us to explore the functional relevance of genes in a defined network. netbox was used to explore the subtype-specific modules in a defined literature curated human interaction […]

2012
PMCID: 3493665
PMID: 22986455
DOI: 10.1007/s00262-012-1354-x

[…] recently tools were developed to address which cancer genome alterations are functionally important, what pathways are affected, or what are the mutations likely to be drivers in tumor progression (netbox [], drivernet [], memo [], paradigm [], chasm [], gistic [], varscan2 [], conexic [])., in summary, to gain further insight into a disease state and suggest treatment strategies integrative […]


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NetBox in publications

 (15)
PMCID: 5756345
PMID: 29304754
DOI: 10.1186/s12864-017-4423-x

[…] method, we compared our results and those obtained by other well-validated computational methods used to identify cancer driver genes, such as activedriver [], dendrix [], mdpfinder [], simon [], netbox [], oncodrivefm [], mutsigcv [], memo [], comdp [], dawnrank [], drivernet [], e-driver [], ipac [], msea [], and oncodriveclust []., we applied driverdb [] to obtain results […]

PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] use a genome-scale protein-protein interaction network. several computational methods that combine mutation data and networks to infer gene sets have been designed. a first class of methods (e.g., netbox; cerami et al., ) looks for significant network modules among a list of genes which is provided as input. such approaches require to define a score threshold to include genes in the analysis, […]

PMCID: 5415494
PMID: 28492066
DOI: 10.1016/j.heliyon.2017.e00277

[…] than 20 driver genes for some cancers. driverdb assembles together lists of the top ranked driver genes determined from the use of 15 packages, including activedriver, dendrix, mdpfinder, simon, netbox, oncodrivefm, mutsigcv, memo, comdp, dawnrank, drivernet, e-driver, ipac, msea, and oncodriveclust. lists the cancer types, sample size, and descriptions of the driver genes used, including […]

PMCID: 5215607
PMID: 27863091
DOI: 10.1002/wsbm.1364

[…] on the final results of a network‐based analysis., biological networks have been used in many cancer‐specific studies, , , , and in order to detect patterns across several cancer types., , , netbox was one of the first network‐based approaches that attempted to distinguish driver from passenger mutations in glioblastoma. it maps genetically aberrant genes [snvs or copy number variations […]

PMCID: 5103929
PMID: 27899990
DOI: 10.3892/ol.2016.5122

[…] functional analysis using the database for annotation, visualization, and integrated discovery online tool. a protein-protein interaction (ppi) network of degs and linker genes was constructed using netbox software and modules were also mined. functional annotation was performed for modules with a maximum number of nodes. subsequent to meta-analysis to pool the data, one dataset that included […]


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NetBox institution(s)
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
NetBox funding source(s)
Supported by National Cancer Institute grants (1R21CA135870-01, U24CA126543, TCGA Cancer Genome Characterization Center), and the Tri-Institutional Training Program in Computational Biology and Medicine.

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