DriverNet protocols

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DriverNet specifications

Information


Unique identifier OMICS_05319
Name DriverNet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Sohrab P. Shah <>

Publication for DriverNet

DriverNet in pipeline

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

[…] 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 analysis […]

DriverNet in publications

 (15)
PMCID: 5940219
PMID: 29738578
DOI: 10.1371/journal.pone.0196939

[…] data., some recent studies have started to explore transcriptome data for systematic prediction of cancer drivers. these studies are limited in several important ways. methods such as moca [] and drivernet [] examined mutations at gene levels, ignoring the functional difference of the mutations within a gene. methods such as xseq [] measured the effects of individual mutations in gene […]

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

[…] 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 from all these algorithms and the cancer datasets considered by our computation […]

PMCID: 5601632
PMID: 28938536
DOI: 10.18632/oncotarget.19481

[…] carcinoma (hnsc), thyroid carcinoma (thca) and kidney renal clear cell carcinoma (kirc)) from the cancer genome atlas (tcga), by comparing the precision, recall and f1 score, our method outperformed drivernet and muffinn in all three datasets. in addition, our method was less affected by protein length compared with drivernet. lastly, our method not only identified the known cancer genes […]

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

[…] 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 chromosome location, gene ontology nomenclature, […]

PMCID: 5274523
PMID: 28149674
DOI: 10.7717/peerj.2568

[…] highly dependent on the quality and size of the pathway interaction network employed, and require a powerful statistical environment for analyses. a number of genomic libraries are available in r. drivernet and dawnrank employ pathway-based methods that use gene interaction graphs in matrix form. we investigated the benefit of combining data from 3 different sources on the prediction outcome […]

DriverNet institution(s)
Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada; Faculty of Information Technology, Monash University, Wellington Road, Clayton, VIC, Australia; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada; Bioinformatics Training Program, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Centre for Translational and Applied Genomics, BC Cancer Agency,Vancouver, BC, Canada; Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
DriverNet funding source(s)
Supported by the BC Cancer Foundation, Canadian Breast Cancer Foundation, Eli-Lilly Canada, Michael Smith Foundation for Health Research, and the Canadian Cancer Society (grant no. 2012-701125).

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